RetrogeneDB ID:

retro_hsap_69

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:51900394..51902416(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000141200
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF2A
Ensembl ID:ENSG00000068796
Aliases:None
Description:kinesin heavy chain member 2A [Source:HGNC Symbol;Acc:6318]


Retrocopy-Parental alignment summary:






>retro_hsap_69
ATGGCCAGCCAGTTCTGCCTCCCTGAATCCCCATGTCTCTCGCCCCTGAAACCCTTGAAGCCACATTTCGGAGACATCCA
AGAGGGCATCTACGTGGCGATCCAGCGCAGTGACAAGCGGATCCACCTCGCTGTGGTCACGGAGATCAACAGAGAAAACT
ATTGGGTCACGGTAGAGTGGGTGGAGAAAGCAGTCAAAAAAGGCAAGAAGATTGACCTGGAGACCATACTCCTGCTGAAT
CCAGCTCTGGACTCTGCTGAACACCCCATGCCGCCCCCGCCCTTATCCCCCTTGGCTCTGGCGCCCTCTTCGGCCATCAG
GGACCAGCGTACCGCCACGAAATGGGTTGCGATGATCCCCCAGAAAAACCAAACAGCCTCAGGGGACAGCCTGGATGTGA
GGGTCCCCAGCAAACCTTGTCTGATGAAGCAGAAAAAGTCTCCCTGCCTCTGGGAAATCCAGAAACTGCAGGAGCAGCGG
GAAAAGCGCAGGCGGCTGCAGCAGGAGATCCGAGCTAGACGCGCCCTCGATGTCAATACCAGAAACCCCAACTACGAAAT
CATGCACATGATCGAAGAGTATCGCAGGCACCTGGACAGCAGCAAGATCTCAGTCCTGGAGCCCCCGCAAGAACATCGCA
TCTGCGTCTGCGTGAGGAAGCGGCCTCTCAACCAGCGAGAGACAACCTTAAAGGACCTGGATATCATCACCGTCCCCTCG
GACAATGTGGTTATGGTGCATGAGTCCAAGCAAAAGGTGGACCTCACTCGCTACCTGCAGAACCAGACCTTCTGCTTCGA
CCATGCCTTCGATGACAAAGCCTCCAACGAGTTGGTGTACCAGTTCACCGCCCAGCCACTGGTGGAGTCCATCTTCCGCA
AGGGCATGGCCACCTGCTTTGCCTATGGGCAGACGGGAAGTGGGAAGACGTACACCATGGGTGGAGACTTTTCAGGAACG
GCCCAAGATTGTTCTAAGGGCATTTATGCTCTGGTGGCACAGGATGTCTTTCTCCTGCTCAGAAACTCCACATATGAGAA
GCTGGACCTCAAAGTCTATGGGACATTTTTTGAGATTTATGGGGGCAAGGTGTATGATTTGTTGAACTGGAAGAAGAAGC
TGCAAGTCCTTGAGGATGGCAATCAGCAAATCCAAGTGGTCGGGCTGCAGGAGAAAGAGGTGTGTTGTGTGGAGGAAGTG
CTGAACCTGGTGGAAATAGGGAATAGCTGTCGGACTTCCAGGCAAACACCTGTCAACGCTCACTCATCCAGGAGCCATGC
AGTGTTCCAGATCATCCTGAAGTCAGGACGGATAATGCATGGCAAGTTTTCCCTCGTTGATTTAGCTGGGAATGAAAGAG
GAGCAGATACAACCAAGGCCAGCCGGAAAAGGCAGCTGGAAGGGGCAGAGATTAACAAGAGTCTTCTAGCCCTCAAAGAA
TGTATTCTGGCTTTGGGTCAGAACAAGCCTCACACCCCATTCAGAGCCAGCAAACTCACACTGGTGCTCCGGGACTCCTT
TATAGGCCAGAACTCCTCCACTTGCATGATTGCTACCATCTCTCCGGGGATGACCTCTTGTGAAAACACTCTCAACACTT
TAAGATATGCAAACAGAGTAAAAAAATTAAATGTAGATGTAAGGCCCTACCATCGTGGCCACTATCCGATTGGACATGAG
GCACCAAGGATGTTAAAAAGTCACATCGGAAATTCAGAAATGTCCCTTCAGAGGGATGAATTTATTAAAATACCTTATGT
ACAGAGTGAGGAGCAGAAAGAGATTGAAGAGGTTGAAACATTACCCACTCTGTTAGGGAAGGATACCACAATTTCAGGGA
AGGGATCTAGCCAATGGCTGGAAAACATCCAGGAGAGAGCTGGTGGAGTACACCATGATATTGATTTTTGCATTGCCCGG
TCTTTGTCCATTTTGGAGCAGAAAATTGATGCTCTGACCGAGATCCAAAAGAAACTGAAATTATTACTAGCTGACCTCCA
CGTGAAGAGCAAGGTAGAGTGA

ORF - retro_hsap_69 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.19 %
Parental protein coverage: 57.08 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHR
..KS.C..E..KLQE.REKRR..QQE.R..RA.DV...NPNYEIM.MI...R..LD........P..EHR
RetrocopyQKKSPCLWEIQKLQEQREKRRRLQQEIRARRALDVNTRNPNYEIMHMIEEYRRHLDSSKISVLEPPQEHR
ParentalICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
ICVCVRKRPLN..ET..KDLD.IT.PS..VVMVHE.KQKVDLTRYL.NQTF.FD.AFDD.A.NE.VY.FT
RetrocopyICVCVRKRPLNQRETTLKDLDIITVPSDNVVMVHESKQKVDLTRYLQNQTFCFDHAFDDKASNELVYQFT
ParentalARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
A.PLVE.IF..GMATCFAYGQTGSGKT.TMGGDFSG..QDCSKGIYAL.A.DVFL.L....Y.KL.L.VY
RetrocopyAQPLVESIFRKGMATCFAYGQTGSGKTYTMGGDFSGTAQDCSKGIYALVAQDVFLLLRNSTYEKLDLKVY
ParentalATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSS
.TFFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGLQE.EV.CVE.VL.L..IGNSCRTS.QT..NAHSS
RetrocopyGTFFEIYGGKVYDLLNWKKKLQVLEDGNQQIQVVGLQEKEVCCVEEVLNLVEIGNSCRTSRQTPVNAHSS
ParentalRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
RSHAVFQIIL......HGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECI.ALG.NKPHTP
RetrocopyRSHAVFQIILKSGRIMHGKFSLVDLAGNERGADTTKASRKRQLEGAEINKSLLALKECILALGQNKPHTP
ParentalFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKELTVD
FRASKLT.VLRDSFIG.NS.TCMIATISPGM.SCENTLNTLRYANRVK.L.VD
RetrocopyFRASKLTLVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYANRVKKLNVD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .12 RPM 25 .94 RPM
bodymap2_adrenal 0 .08 RPM 28 .53 RPM
bodymap2_brain 0 .00 RPM 98 .96 RPM
bodymap2_breast 0 .00 RPM 22 .90 RPM
bodymap2_colon 0 .00 RPM 27 .69 RPM
bodymap2_heart 0 .00 RPM 8 .62 RPM
bodymap2_kidney 0 .00 RPM 18 .26 RPM
bodymap2_liver 0 .00 RPM 4 .39 RPM
bodymap2_lung 0 .00 RPM 25 .79 RPM
bodymap2_lymph_node 0 .00 RPM 34 .85 RPM
bodymap2_ovary 0 .00 RPM 46 .63 RPM
bodymap2_prostate 0 .00 RPM 23 .16 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .75 RPM
bodymap2_testis 78 .98 RPM 95 .02 RPM
bodymap2_thyroid 0 .00 RPM 28 .21 RPM
bodymap2_white_blood_cells 0 .00 RPM 126 .40 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_69 was not detected

EST - click to see more details

105 EST(s) were mapped to retro_hsap_69 retrocopy
EST ID Start End Identity Match Mis-match Score
BF979470 51900290 51900993 97.4 672 3 651
BG717678 51900302 51900944 98.6 637 4 630
BG719749 51900306 51900942 99.6 631 3 626
BG721597 51900287 51901029 99.6 738 2 734
BG771992 51900306 51901110 99.2 788 6 775
BG772495 51900266 51901053 96.4 776 10 754
BI461290 51900306 51901088 97.9 772 5 758
BI462018 51900283 51900974 98.4 680 5 663
BI462901 51900290 51901142 97.9 806 13 786
BI463904 51900292 51900970 99.6 675 3 672
BI464561 51900306 51900907 98 593 4 580
BI561657 51900306 51901162 96 829 16 796
BI829106 51900300 51901019 99.6 719 0 718
BM560261 51900276 51901169 97.2 883 6 864
BP371564 51900289 51901010 99.9 581 1 579
BP371589 51900936 51901604 99.9 567 1 565
CD171892 51900328 51901130 98.6 799 3 792
CD244601 51900427 51901269 97.9 840 2 829
CD299965 51900313 51901159 98.4 844 2 836
CD634108 51900475 51901008 99.9 532 1 531
CD634109 51900299 51901008 99.2 708 1 705
CD634110 51900299 51901008 99.8 706 2 703
CD634111 51900299 51901008 99.9 708 1 707
CD634112 51900299 51900978 99 672 4 662
CD634113 51900288 51901008 99.4 718 1 714
CD634114 51900288 51901008 98.7 717 2 710
CD634115 51900299 51901008 99.5 708 1 706
CD634116 51900288 51901008 98.9 716 3 710
CD634117 51900299 51900922 99.9 622 1 621
CV030651 51900394 51901003 100 609 0 609
DB020022 51900481 51901036 99.9 554 1 553
DB020310 51900269 51900900 99.7 571 1 568
DB022664 51900287 51900843 99.3 555 1 553
DB022991 51900287 51900853 99.9 565 1 564
DB024150 51900287 51900835 100 548 0 548
DB024991 51900291 51900848 99.9 556 1 555
DB026207 51900283 51900839 100 556 0 556
DB027113 51900296 51900834 99.9 537 1 536
DB027216 51900288 51901057 99.9 600 1 598
DB027224 51900306 51900904 100 598 0 598
DB027590 51900307 51900884 100 577 0 577
DB028384 51900296 51900839 99.9 542 1 541
DB028704 51900289 51900870 99.9 580 1 579
DB029624 51900289 51900880 100 591 0 591
DB029947 51900277 51900880 100 603 0 603
DB030135 51900306 51900903 99.7 571 1 568
DB031001 51900306 51900873 99.9 566 1 565
DB031046 51900552 51901124 99.7 570 2 568
DB031435 51900275 51900884 99.7 607 2 605
DB031441 51900306 51900929 100 623 0 623
DB033974 51900296 51900866 99.7 568 2 566
DB034169 51900287 51900881 100 594 0 594
DB034667 51900306 51900886 99.9 579 1 578
DB035029 51900306 51900858 99.9 551 1 550
DB035419 51900301 51900851 99.9 549 1 548
DB035778 51900287 51900862 99.9 574 1 573
DB036627 51900287 51900863 100 576 0 576
DB038024 51900306 51900881 99.9 574 1 573
DB038823 51900306 51900881 100 574 0 574
DB040581 51900306 51900868 99.7 559 1 556
DB040676 51900306 51900868 99.9 561 1 560
DB041512 51900287 51900840 99.7 551 2 549
DB041680 51900287 51900835 99.9 547 1 546
DB042083 51900619 51901199 98.8 578 2 574
DB042261 51900306 51900897 99.7 589 2 587
DB042755 51900306 51900858 99.5 552 0 551
DB042765 51900287 51900843 99.7 554 2 552
DB043236 51900287 51900862 99.9 574 1 573
DB043273 51900287 51900863 100 576 0 576
DB043535 51900306 51900865 99.9 558 1 557
DB044392 51900289 51900845 99.9 555 1 554
DB044824 51900301 51900853 99.9 551 1 550
DB044886 51900287 51900850 99.5 560 3 557
DB045217 51900287 51900848 100 561 0 561
DB045293 51900927 51901498 99.9 570 1 569
DB045885 51900306 51900859 99.9 552 1 551
DB045896 51900306 51900864 100 558 0 558
DB045982 51900306 51900877 99.9 570 1 569
DB046738 51900287 51900852 99.9 564 1 563
DB047467 51900289 51900855 100 566 0 566
DB047630 51900306 51900883 99.9 576 1 575
DB047718 51900296 51900845 99.9 548 1 547
DB048033 51900306 51900856 100 550 0 550
DB048739 51900287 51900871 99.9 583 1 582
DB049910 51900283 51900847 99.9 563 1 562
DB050148 51900287 51900863 99.7 574 2 572
DB050845 51900300 51900858 99.9 557 1 556
DB051208 51900306 51900889 99.9 582 1 581
DB052193 51900306 51900866 99.9 559 1 558
DB053072 51900306 51900875 100 569 0 569
DB053423 51900287 51900841 100 554 0 554
DB056105 51900304 51900860 99.7 554 2 552
DB056441 51900296 51900817 99.9 520 1 519
DB057938 51900306 51900838 99.9 531 1 530
DB058724 51900289 51900832 100 543 0 543
DB060434 51900287 51900839 99.9 551 1 550
DB089298 51900306 51900868 99.9 561 1 560
DB093988 51900283 51900839 99.9 555 1 554
DB446880 51900323 51900761 99.6 436 1 433
DB456589 51900314 51900795 99.6 479 2 477
DB459465 51900306 51900793 99.2 486 1 484
DC396938 51900306 51901233 99.9 573 1 569
DC398892 51900306 51901088 99.9 550 1 548
HY012274 51900306 51900828 98.9 515 6 509
HY212815 51901082 51901565 99.6 481 2 479

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_607751811 libraries 13 libraries 2 libraries 0 libraries 3 libraries
TSS #2 TSS_607761824 libraries 3 libraries 2 libraries 0 libraries 0 libraries
TSS #3 TSS_607771825 libraries 1 library 2 libraries 1 library 0 libraries

The graphical summary, for retro_hsap_69 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_69 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_69 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_88
Equus caballus retro_ecab_32
Parental genes homology:
Parental genes homology involve 24 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000095191 retrocopy
retro_apla_3,
Bos taurus ENSBTAG000000150221 retrocopy
retro_btau_180,
Choloepus hoffmanni ENSCHOG000000078881 retrocopy
retro_chof_1348,
Cavia porcellus ENSCPOG000000093931 retrocopy
retro_cpor_72,
Dipodomys ordii ENSDORG000000063351 retrocopy
retro_dord_763,
Equus caballus ENSECAG000000198101 retrocopy
retro_ecab_32,
Homo sapiens ENSG00000068796 1 retrocopy
retro_hsap_69 ,
Gorilla gorilla ENSGGOG000000047741 retrocopy
retro_ggor_68,
Macaca mulatta ENSMMUG000000003991 retrocopy
retro_mmul_145,
Monodelphis domestica ENSMODG000000196051 retrocopy
retro_mdom_242,
Mus musculus ENSMUSG000000216931 retrocopy
retro_mmus_68,
Nomascus leucogenys ENSNLEG000000028651 retrocopy
retro_nleu_2329,
Oryctolagus cuniculus ENSOCUG000000104661 retrocopy
retro_ocun_156,
Otolemur garnettii ENSOGAG000000005275 retrocopies
retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Ochotona princeps ENSOPRG000000117681 retrocopy
retro_opri_815,
Procavia capensis ENSPCAG000000050891 retrocopy
retro_pcap_22,
Rattus norvegicus ENSRNOG000000140002 retrocopies
retro_rnor_1284, retro_rnor_47,
Sorex araneus ENSSARG000000077681 retrocopy
retro_sara_457,
Sarcophilus harrisii ENSSHAG000000019501 retrocopy
retro_shar_30,
Ictidomys tridecemlineatus ENSSTOG000000127101 retrocopy
retro_itri_40,
Tupaia belangeri ENSTBEG000000093961 retrocopy
retro_tbel_761,
Tarsius syrichta ENSTSYG000000021151 retrocopy
retro_tsyr_1791,
Vicugna pacos ENSVPAG000000088641 retrocopy
retro_vpac_572,
Drosophila melanogaster FBgn00302682 retrocopies
retro_dmel_1, retro_dmel_2,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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