RetrogeneDB ID:

retro_hsap_42

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:59499139..59500285(+)
Located in intron of:ENSG00000157483
Retrocopy
information
Ensembl ID:ENSG00000171989
Aliases:LDHAL6B, LDH6B, LDHAL6, LDHL
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHAL6A
Ensembl ID:ENSG00000166800
Aliases:LDHAL6A, LDH6A
Description:lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:28335]


Retrocopy-Parental alignment summary:






>retro_hsap_42
ATGAGTTGGACTGTGCCTGTTGTGCGGGCCAGCCAGAGAGTGAGCTCGGTGGGAGCGAATTTCCTATGCCTGGGGATGGC
CCTGTGTCCGCGTCAAGCAACGCGCATCCCGCTCAACGGCACCTGGCTCTTCACCCCCGTGAGCAAGATGGCGACTGTGA
AGAGTGAGCTTATTGAGCGTTTCACTTCCGAGAAGCCCGTTCATCACAGTAAGGTCTCCATCATAGGAACTGGATCGGTG
GGCATGGCCTGCGCTATCAGCATCTTATTAAAAGGCTTGAGTGATGAACTTGCCCTTGTGGATCTTGATGAAGACAAACT
GAAGGGTGAGACGATGGATCTTCAACATGGCAGCCCTTTCACGAAAATGCCAAATATTGTTTGTAGCAAAGATTACTTTG
TCACAGCAAACTCCAACCTAGTGATTATCACAGCAGGTGCACGCCAAGAAAAGGGAGAAACGCGCCTTAATTTAGTCCAG
CGAAATGTGGCCATCTTCAAGTTAATGATTTCCAGTATTGTCCAGTACAGCCCCCACTGCAAACTGATTATTGTTTCCAA
TCCAGTGGATATCTTAACTTATGTAGCTTGGAAGTTGAGTGCATTTCCCAAAAACCGTATTATTGGAAGCGGCTGTAATC
TGGATACTGCTCGTTTTCGTTTCTTGATTGGACAAAAGCTTGGTATCCATTCTGAAAGCTGCCATGGATGGATCCTCGGA
GAGCATGGAGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAACATAGCTGGTGTCCCTTTGAAGGATCTGAACTCTGATAT
AGGAACTGATAAAGATCCTGAGCAATGGAAAAATGTCCACAAAGAAGTGACTGCAACTGCCTATGAGATTATTAAAATGA
AAGGTTATACTTCTTGGGCCATTGGCCTATCTGTGGCCGATTTAACAGAAAGTATTTTGAAGAATCTTAGGAGAATACAT
CCAGTTTCCACCATAATTAAGGGCCTCTATGGAATAGATGAAGAAGTATTCCTCAGTATTCCTTGTATCCTGGGAGAGAA
CGGTATTACCAACCTTATAAAGATAAAGCTGACCCCTGAAGAAGAGGCCCATCTGAAAAAAAGTGCAAAAACACTCTGGG
AAATTCAGAATAAGCTTAAGCTTTAA

ORF - retro_hsap_42 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.23 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMATIKSELIKNFAEEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDVDEGKLKGETMDLQHGSP
MAT.KSELI..F..E...HH.K.SI.GTGSVG.ACAISILLKGLSDEL.LVD.DE.KLKGETMDLQHGSP
RetrocopyMATVKSELIERFTSEKPVHHSKVSIIGTGSVGMACAISILLKGLSDELALVDLDEDKLKGETMDLQHGSP
ParentalFMKMPNIVSSKDYLVTANSNLVIITAGARQKKGETRLDLVQRNVSIFKLMIPNITQYSPHCKLLIVTNPV
F.KMPNIV.SKDY.VTANSNLVIITAGARQ.KGETRL.LVQRNV.IFKLMI..I.QYSPHCKL.IV.NPV
RetrocopyFTKMPNIVCSKDYFVTANSNLVIITAGARQEKGETRLNLVQRNVAIFKLMISSIVQYSPHCKLIIVSNPV
ParentalDILTYVAWKLSGFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNIAGVP
DILTYVAWKLS.FPKNR.IGSGCNLD.ARFR..IGQ.LGIHSESCHG.ILGEHGDSSVPVWSGVNIAGVP
RetrocopyDILTYVAWKLSAFPKNRIIGSGCNLDTARFRFLIGQKLGIHSESCHGWILGEHGDSSVPVWSGVNIAGVP
ParentalLKDLNPDIGTDKDPEQWENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPVSTLSKGL
LKDLN.DIGTDKDPEQW.NVHK.V....YE..KMKGYTSW.I.LSVADLTESILKNLRR.HPVST..KGL
RetrocopyLKDLNSDIGTDKDPEQWKNVHKEVTATAYEIIKMKGYTSWAIGLSVADLTESILKNLRRIHPVSTIIKGL
ParentalYGINEDIFLSVPCILGENGITDLIKVKLTLEEEACLQKSAETLWEIQKELKL
YGI.E..FLS.PCILGENGIT.LIK.KLT.EEEA.L.KSA.TLWEIQ..LKL
RetrocopyYGIDEEVFLSIPCILGENGITNLIKIKLTPEEEAHLKKSAKTLWEIQNKLKL

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 .58 RPM 0 .24 RPM
bodymap2_adrenal 0 .41 RPM 0 .84 RPM
bodymap2_brain 0 .14 RPM 0 .59 RPM
bodymap2_breast 0 .12 RPM 0 .16 RPM
bodymap2_colon 0 .33 RPM 0 .04 RPM
bodymap2_heart 0 .02 RPM 0 .06 RPM
bodymap2_kidney 0 .25 RPM 0 .97 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .27 RPM
bodymap2_ovary 0 .12 RPM 0 .71 RPM
bodymap2_prostate 0 .33 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .11 RPM 0 .00 RPM
bodymap2_testis 16 .40 RPM 7 .33 RPM
bodymap2_thyroid 0 .15 RPM 0 .79 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .45 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_42 was not detected

EST - click to see more details

30 EST(s) were mapped to retro_hsap_42 retrocopy
EST ID Start End Identity Match Mis-match Score
AW953921 59499106 59499693 98.5 574 8 560
BG718803 59499064 59499666 100 602 0 602
BP368794 59499092 59499645 97.3 535 15 520
BU561631 59499073 59499702 97.8 624 4 614
CV024257 59499139 59499776 99.1 632 3 628
CV375046 59499138 59499593 98.1 446 7 435
DB021204 59499107 59499589 98.4 477 3 472
DB021438 59499067 59499617 99 547 3 543
DB022472 59499061 59499618 99.5 557 0 556
DB024248 59499061 59499621 99.5 557 3 554
DB025209 59499061 59499559 99.4 494 3 491
DB027291 59499064 59499649 99.5 582 3 579
DB032702 59499032 59499570 99.9 537 1 536
DB035729 59499103 59499685 100 581 0 581
DB041618 59499049 59499613 99.5 561 3 558
DB042270 59499064 59499619 98.8 551 4 546
DB046642 59499064 59499603 99.5 536 3 533
DB052936 59499064 59499627 99.2 558 5 553
DB055157 59499068 59499622 99 551 3 547
DB441948 59499071 59499492 97.4 415 4 406
DB442183 59499064 59499497 98 427 4 418
DB446851 59499071 59499512 99.4 438 3 435
DB452514 59499073 59499559 99.2 482 4 478
HY008337 59499069 59499602 99.3 529 4 525
HY010322 59499072 59499570 99.6 496 2 494
HY010617 59499107 59499668 99.7 559 2 557
HY015264 59499064 59499593 99.3 525 4 521
HY026718 59499064 59499551 100 486 0 486
HY047922 59499107 59499563 99.8 455 1 454
HY243389 59499107 59499527 100 420 0 420

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_450761824 libraries2 libraries1 library0 libraries2 libraries
TSS #2 TSS_450771822 libraries3 libraries1 library0 libraries3 libraries
TSS #3 TSS_450781823 libraries3 libraries2 libraries1 library0 libraries

The graphical summary, for retro_hsap_42 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_42 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_42 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_62
Pongo abelii retro_pabe_203
Macaca mulatta retro_mmul_261
Callithrix jacchus retro_cjac_164
Parental genes homology:
Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000070672 retrocopies
retro_cjac_164, retro_cjac_2180,
Homo sapiens ENSG000001117161 retrocopy
retro_hsap_4863,
Homo sapiens ENSG000001343335 retrocopies
retro_hsap_2097, retro_hsap_2285, retro_hsap_3021, retro_hsap_323, retro_hsap_4231,
Homo sapiens ENSG00000166800 2 retrocopies
retro_hsap_42 , retro_hsap_905,
Macaca mulatta ENSMMUG000000146142 retrocopies
retro_mmul_1111, retro_mmul_261,
Nomascus leucogenys ENSNLEG000000177802 retrocopies
retro_nleu_29, retro_nleu_378,
Otolemur garnettii ENSOGAG000000092611 retrocopy
retro_ogar_2662,
Pongo abelii ENSPPYG000000034352 retrocopies
retro_pabe_203, retro_pabe_779,
Pan troglodytes ENSPTRG000000034231 retrocopy
retro_ptro_62,
Tarsius syrichta ENSTSYG000000080624 retrocopies
retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,

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 ) > 0 RPM = 0.7 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .26 RPM
CEU_NA11843 0 .37 RPM
CEU_NA11930 0 .46 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .27 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .24 RPM
CEU_NA12872 0 .33 RPM
CEU_NA12873 0 .57 RPM
FIN_HG00183 0 .33 RPM
FIN_HG00277 0 .48 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .24 RPM
FIN_HG00338 0 .30 RPM
FIN_HG00349 0 .34 RPM
FIN_HG00375 0 .34 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .25 RPM
GBR_HG00099 0 .32 RPM
GBR_HG00111 0 .24 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .24 RPM
GBR_HG00131 0 .34 RPM
GBR_HG00133 0 .19 RPM
GBR_HG00134 0 .70 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .39 RPM
GBR_HG00143 0 .19 RPM
TSI_NA20512 0 .11 RPM
TSI_NA20513 0 .31 RPM
TSI_NA20518 0 .14 RPM
TSI_NA20532 0 .58 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .20 RPM
TSI_NA20765 0 .37 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .21 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .34 RPM
YRI_NA18907 0 .31 RPM
YRI_NA18916 0 .36 RPM
YRI_NA19093 0 .42 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .47 RPM
YRI_NA19118 0 .27 RPM
YRI_NA19213 0 .41 RPM
YRI_NA19214 0 .20 RPM
YRI_NA19223 0 .48 RPM

Indel association:

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



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