RetrogeneDB ID:

retro_hsap_2422

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:20:30135306..30135849(+)
Located in intron of:ENSG00000101294
Retrocopy
information
Ensembl ID:ENSG00000101898
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MCTS1
Ensembl ID:ENSG00000232119
Aliases:None
Description:malignant T cell amplified sequence 1 [Source:HGNC Symbol;Acc:23357]


Retrocopy-Parental alignment summary:






>retro_hsap_2422
ATGTTCAAGAAGTTTGATGAAAAGGAAAGTGTGTCCAACTGCATCCAGTTGAAAACGTCAGTTATTAAGGGCATTAAGAG
CCAACTGGTAGAGCAATTTCCAGGTATTGAACCATGGCTTAATCAAATCATGCCTAAGAAAGATCCTGTCAAAATAGTCC
GATGCCACGAACATACAGAAATCCTTACCGTAAGTGGGGAATTATTGTTTTTTAGACAAAGAAAGGGGCCTTTTTGTCCA
ACTCTAAGGTTGCTTCACAAATACCCTTTTATCCTGCCACACCAGCAGGTTGATAAAGGAGCTATCAAATTTGTACTCAG
TGGCGCAAATATTATGTGTCCAGGTTTAACTTCTCCTGGAGCTAAGCTGTACCCTGCTGCAGTAGATACGATTGTAGCAG
TCACAGCGGAAGGAAAACAGCATGCTCTGTGTGTTGGGGTCATGAAGATGTCTGCAGAAGATATTGAGAAAGTCAACAAA
GGAATTGGCATTGAAAATATCCATTATTTAAATGATGGGCTGTGGCACATGAAGACATATAAA

ORF - retro_hsap_2422 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.03 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
MFKKFDEKE.VSNCIQLKTSVIKGIK.QL.EQFPGIEPWLNQIMPKKDPVKIVRCHEH.EILTV.GELLF
RetrocopyMFKKFDEKESVSNCIQLKTSVIKGIKSQLVEQFPGIEPWLNQIMPKKDPVKIVRCHEHTEILTVSGELLF
ParentalFRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAIMAEGKQ
FRQR.GPF.PTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVA..AEGKQ
RetrocopyFRQRKGPFCPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAVTAEGKQ
ParentalHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
RetrocopyHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK

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 1 .03 RPM 16 .26 RPM
bodymap2_adrenal 2 .01 RPM 18 .38 RPM
bodymap2_brain 1 .31 RPM 18 .21 RPM
bodymap2_breast 0 .72 RPM 23 .29 RPM
bodymap2_colon 1 .10 RPM 22 .74 RPM
bodymap2_heart 0 .70 RPM 16 .01 RPM
bodymap2_kidney 0 .60 RPM 26 .20 RPM
bodymap2_liver 0 .34 RPM 29 .21 RPM
bodymap2_lung 1 .02 RPM 15 .51 RPM
bodymap2_lymph_node 1 .48 RPM 22 .92 RPM
bodymap2_ovary 3 .08 RPM 15 .02 RPM
bodymap2_prostate 0 .94 RPM 22 .38 RPM
bodymap2_skeletal_muscle 0 .53 RPM 12 .66 RPM
bodymap2_testis 1 .73 RPM 20 .96 RPM
bodymap2_thyroid 1 .75 RPM 14 .84 RPM
bodymap2_white_blood_cells 0 .35 RPM 26 .01 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2422 in 48 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CGN POLR2A 20:30135101..30135364
ENCFF002CHO POLR2A 20:30134756..30135447
ENCFF002CIH POLR2A 20:30134806..30135382
ENCFF002CIO POLR2A 20:30134880..30135425
ENCFF002CJE POLR2A 20:30134821..30135491
ENCFF002CJZ POLR2A 20:30134816..30135463
ENCFF002CKX POLR2A 20:30134874..30135409
ENCFF002CLM POLR2A 20:30134966..30135506
ENCFF002CMI POLR2A 20:30134806..30135433
ENCFF002COJ POLR2A 20:30134992..30135428
ENCFF002CPG POLR2A 20:30135130..30135359
ENCFF002CPH POLR2A 20:30134867..30135257
ENCFF002CQA POLR2A 20:30135172..30135368
ENCFF002CQC POLR2A 20:30135093..30135376
ENCFF002CQE POLR2A 20:30134995..30135355
ENCFF002CQG POLR2A 20:30135098..30135337
ENCFF002CQI POLR2A 20:30135086..30135378
ENCFF002CQK POLR2A 20:30134957..30135390
ENCFF002CQM POLR2A 20:30135045..30135380
ENCFF002CQO POLR2A 20:30134942..30135370
ENCFF002CRK POLR2A 20:30134999..30135523
ENCFF002CRO POLR2A 20:30134996..30135416
ENCFF002CSY POLR2A 20:30134805..30135511
ENCFF002CUP POLR2A 20:30135136..30135270
ENCFF002CUQ POLR2A 20:30134798..30135414
ENCFF002CVF POLR2A 20:30135029..30135445
ENCFF002CVJ POLR2A 20:30134864..30135165
ENCFF002CVJ POLR2A 20:30135163..30135399
ENCFF002CXM POLR2A 20:30134815..30135305
ENCFF002CXN POLR2A 20:30134796..30135292
ENCFF002CXN POLR2A 20:30134997..30135493
ENCFF002CXO POLR2A 20:30135038..30135462
ENCFF002CXP POLR2A 20:30135104..30135233
ENCFF002CXR POLR2A 20:30135094..30135264
ENCFF002CZC POLR2A 20:30134846..30135454
ENCFF002CZD POLR2A 20:30134899..30135401
ENCFF002CZQ POLR2A 20:30135065..30135345
ENCFF002CZW POLR2A 20:30134838..30135494
ENCFF002CZY POLR2A 20:30134911..30135392
ENCFF002DAH POLR2A 20:30135056..30135340
ENCFF002DAK POLR2A 20:30135009..30135509
ENCFF002DAS POLR2A 20:30134973..30135449
ENCFF002DAV POLR2A 20:30135094..30135263
ENCFF002DAY POLR2A 20:30134917..30135553
ENCFF002DBB POLR2A 20:30135131..30135331
ENCFF002DBE POLR2A 20:30135193..30135317
ENCFF002DBO POLR2A 20:30135064..30135318
ENCFF002DBP POLR2A 20:30135029..30135359
ENCFF002DBQ POLR2A 20:30134936..30135306
ENCFF002DBT POLR2A 20:30134950..30135320

EST - click to see more details

No EST(s) were mapped for retro_hsap_2422 retrocopy.

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_99479104 libraries33 libraries210 libraries610 libraries872 libraries
TSS #2 TSS_994801079 libraries659 libraries86 libraries3 libraries2 libraries

The graphical summary, for retro_hsap_2422 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

Experiment type: PCR amplification
Forward primer: CCTGCAGGGGACTCCACCGGAGC (23 nt long)
Reverse primer: TTCATCTGTGGTAAGAGCACCC (22 nt long)
Anneling temperature: 63 °C
(Expected) product size: 785
Electrophoresis gel image:
Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Retrocopy orthology:
Retrocopy retro_hsap_2422 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1396
Gorilla gorilla retro_ggor_1507
Pongo abelii retro_pabe_1786
Macaca mulatta retro_mmul_626
Mus musculus retro_mmus_69
Rattus norvegicus retro_rnor_1841
Parental genes homology:
Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000055021 retrocopy
retro_cpor_1411,
Erinaceus europaeus ENSEEUG000000072581 retrocopy
retro_eeur_197,
Echinops telfairi ENSETEG000000154621 retrocopy
retro_etel_19,
Homo sapiens ENSG00000232119 1 retrocopy
retro_hsap_2422 ,
Gorilla gorilla ENSGGOG000000094201 retrocopy
retro_ggor_1507,
Myotis lucifugus ENSMLUG000000151011 retrocopy
retro_mluc_16,
Monodelphis domestica ENSMODG000000103541 retrocopy
retro_mdom_203,
Mus musculus ENSMUSG000000003553 retrocopies
retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Oryctolagus cuniculus ENSOCUG000000143151 retrocopy
retro_ocun_212,
Pan troglodytes ENSPTRG000000222411 retrocopy
retro_ptro_1396,
Pteropus vampyrus ENSPVAG000000132493 retrocopies
retro_pvam_1323, retro_pvam_645, retro_pvam_867,
Rattus norvegicus ENSRNOG000000025632 retrocopies
retro_rnor_1841, retro_rnor_957,
Ictidomys tridecemlineatus ENSSTOG000000114962 retrocopies
retro_itri_1136, retro_itri_1468,
Tupaia belangeri ENSTBEG000000106662 retrocopies
retro_tbel_1485, retro_tbel_4265,
Tarsius syrichta ENSTSYG000000014401 retrocopy
retro_tsyr_55,
Tursiops truncatus ENSTTRG000000072081 retrocopy
retro_ttru_1587,

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 = 4.7 RPM Legend:


Library Retrogene expression
CEU_NA11831 2 .50 RPM
CEU_NA11843 2 .13 RPM
CEU_NA11930 3 .72 RPM
CEU_NA12004 3 .87 RPM
CEU_NA12400 2 .00 RPM
CEU_NA12751 3 .38 RPM
CEU_NA12760 3 .19 RPM
CEU_NA12827 3 .44 RPM
CEU_NA12872 3 .84 RPM
CEU_NA12873 4 .02 RPM
FIN_HG00183 3 .38 RPM
FIN_HG00277 2 .40 RPM
FIN_HG00315 2 .79 RPM
FIN_HG00321 3 .17 RPM
FIN_HG00328 3 .03 RPM
FIN_HG00338 3 .11 RPM
FIN_HG00349 3 .98 RPM
FIN_HG00375 3 .77 RPM
FIN_HG00377 3 .45 RPM
FIN_HG00378 3 .55 RPM
GBR_HG00099 3 .60 RPM
GBR_HG00111 2 .94 RPM
GBR_HG00114 2 .76 RPM
GBR_HG00119 3 .07 RPM
GBR_HG00131 3 .13 RPM
GBR_HG00133 3 .28 RPM
GBR_HG00134 3 .10 RPM
GBR_HG00137 2 .39 RPM
GBR_HG00142 4 .03 RPM
GBR_HG00143 3 .67 RPM
TSI_NA20512 2 .29 RPM
TSI_NA20513 4 .04 RPM
TSI_NA20518 3 .08 RPM
TSI_NA20532 3 .98 RPM
TSI_NA20538 4 .70 RPM
TSI_NA20756 2 .82 RPM
TSI_NA20765 3 .71 RPM
TSI_NA20771 3 .74 RPM
TSI_NA20786 3 .71 RPM
TSI_NA20798 3 .62 RPM
YRI_NA18870 3 .72 RPM
YRI_NA18907 3 .33 RPM
YRI_NA18916 3 .47 RPM
YRI_NA19093 4 .45 RPM
YRI_NA19099 3 .70 RPM
YRI_NA19114 3 .41 RPM
YRI_NA19118 4 .18 RPM
YRI_NA19213 2 .54 RPM
YRI_NA19214 3 .39 RPM
YRI_NA19223 3 .70 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017