RetrogeneDB ID:

retro_hsap_560

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:37626345..37627799(+)
Located in intron of:ENSG00000148513
Retrocopy
information
Ensembl ID:ENSG00000237970
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM161B
Ensembl ID:ENSG00000164180
Aliases:TMEM161B, FLB3342, PRO1313
Description:transmembrane protein 161B [Source:HGNC Symbol;Acc:28483]


Retrocopy-Parental alignment summary:






>retro_hsap_560
GTGATAGGTATACAGCTGTTGTTACCATGGTGATGGCCAGTGTCATGCAGAAGATTATACCTCGCTATTCTCTTGCTCAA
TGGCTACTCTGTAATGGCAGTTTGAGGTGGTATCAACATTCTACAGTAGAAGAATCAAGAATTCTTGCAGGGAATCAGCA
AAAAGAGAAAAGCAAAAAAGATAGGAAATATAATGGTCACACTGAAAGTAAGCCATTAACCATTCCAAAGGATATTGACC
TTCGTCTAGAAACAAAGTCAGTTACAGAAGTGGATACATTAGCATTGCATTACTTCCCAGAATACCAGTGACTGGTGGAT
TTCACAGTGGCTGCTACAGTCGTGTATCTAGTAACTGAAGTCGACTACAAGTTTATGAAGCCTACACAGGAAATAAATAT
CAGCTTAGTCTGGTGCCTGCTTGTTTCGTCTTTTGCAATCGAAGTTCTATTTTCATTAATTACACACTATTTTAAAGTAG
AAGATGCTGGTGAAAGATCTGTTTGTGTCACCTTTGGATTTTTTTTCTTTGTCAAAGCAATGGCAGTGTTGATTGTAACA
GAAAATTATCTGGAATTTGGACTTGAAACAGGGTTTACAAATTTTTCAGGCAGTGCGATGCAGTTTCTTGAAAAGCAAGG
TTTAGAATCTCAGAGTCCTGTTTTAAAACTTACTTCCAAATTTTTTCCTGGCTATTTTCTGTTCACTCACTGGGGCTTTT
TTCACATTTCCTGGATTACGGCTGGCTCAAATGCATCTGGATACCCTGAATTTGGCAACAGAAAAAATTACACAAACATT
ATTTCATATCAGCTTCTTGGCACATTTATTTATGGTTCTGCTCTGGGTAAAACCAGTCACCAAAGACTACATTATGAACC
CAACCTTGGGTGAAGAAAGCATCACTTTAATGACAGAAGCCACATTTGGTACTCTGCAAATCTGGTTAATAATCCTGCTG
TGTGCTTTGCGGTTGGCCATGATGCATAGTCACCTGCAAGCTTATTTAAATTTAGCCCAAAAATGTGTGGATCAGATGAA
GAAAGAAGCAGGGTGAATAAGTACAGTTGAGCTACAGAAAATGGTGGCTTGAGTCTTTTATTATCTTTTTGTCATTGCAC
TGCAGTATGTGGTGCCTCTGGTAACACTGTTTCACACAACTCTGCTTTTGAAAACACTAGGTAATCATTCCTGGGGTATT
TATCCAGAATCTGTCTCTACCTTACCAGTGGATAATAGTCTACTCTACAATTCTGTTTACTCTGAATTACCATCAGCTGA
AGAGAAGATGAAGGTTACTGTTACACAAATAACAGTGGCACTGAGCAGCTTAAAAACATTTTTACACTTCTTGTTTTTTG
AGGACTTCTGTCTTTTCTGACCTGGTAGATTGCTGCTTGCCTCTTTTCTACAAGCCTTTTTGGGCTTTTTTATCACCAGT
ATCTGACTGTGGCA

ORF - retro_hsap_560 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.73 %
Parental protein coverage: 99.59 %
Number of stop codons detected: 5
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalVIGIQL-VVTMVMASVMQKIIPHYSLARWLLCNGSLRWYQHPTEEELRILAGKQQKGKTKKDRKYNGHIE
VIGIQL.VVTMVMASVMQKIIP.YSLA.WLLCNGSLRWYQH.T.EE.RILAG.QQK.K.KKDRKYNGH.E
RetrocopyVIGIQL<VVTMVMASVMQKIIPRYSLAQWLLCNGSLRWYQHSTVEESRILAGNQQKEKSKKDRKYNGHTE
ParentalSKPLTIPKDIDLHLETKSVTEVDTLALHYFPEYQWLVDFTVAATVVYLVTEVYYNFMKPTQEMNISLVWC
SKPLTIPKDIDL.LETKSVTEVDTLALHYFPEYQ.LVDFTVAATVVYLVTEV.Y.FMKPTQE.NISLVWC
RetrocopySKPLTIPKDIDLRLETKSVTEVDTLALHYFPEYQ*LVDFTVAATVVYLVTEVDYKFMKPTQEINISLVWC
ParentalLLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFGFFFFVKAMAVLIVTENYLEFGLETGFTNFSDSAMQF
LLV.SFAI.VLFSL.THYFKVED.GERSVCVTFG...FVKAMAVLIVTENYLEFGLETGFTNFS.SAMQF
RetrocopyLLVSSFAIEVLFSLITHYFKVEDAGERSVCVTFGXXXFVKAMAVLIVTENYLEFGLETGFTNFSGSAMQF
ParentalLEKQGLESQSPVSKLTFK-FFLAIFCSFIGAFLTFPGLRLAQMHLDALNLATEKITQTLLHINFLAPLFM
LEKQGLESQSPV.KLT.K.FFLAIFCS..GAF.TFPGLRLAQMHLD.LNLATEKITQTL.HI.FLA.LFM
RetrocopyLEKQGLESQSPVLKLTSK>FFLAIFCSLTGAFFTFPGLRLAQMHLDTLNLATEKITQTLFHISFLAHLFM
ParentalVLLWVKPITKDYIMNPPLGKESIPLMTEATFDTLRLWLIILLCALRLAMMRSHLQAYLNLAQKCVDQMKK
VLLWVKP.TKDYIMNP.LG.ESI.LMTEATF.TL..WLIILLCALRLAMM.SHLQAYLNLAQKCVDQMKK
RetrocopyVLLWVKPVTKDYIMNPTLGEESITLMTEATFGTLQIWLIILLCALRLAMMHSHLQAYLNLAQKCVDQMKK
ParentalEAGRISTVELQKMVARVFYYLCVIALQYVAPLVMLLHTTLLLKTLGNHSWGIYPESISTLPVDNSLLSNS
EAG.ISTVELQKMVA.VFYYL.VIALQYV.PLV.L.HTTLLLKTLGNHSWGIYPES.STLPVDNSLL.NS
RetrocopyEAG*ISTVELQKMVA*VFYYLFVIALQYVVPLVTLFHTTLLLKTLGNHSWGIYPESVSTLPVDNSLLYNS
ParentalVYSELPSAEGKMKVTVTQITVALSS-LKNIFTPLLFRGLLSFLTWWIAACLFSTSLFGLFYHQYLTVA
VYSELPSAE.KMKVTVTQITVALSS.LKNIFT.L.F.GLLSFLTW.IAACLFSTSLFGLFYHQYLTVA
RetrocopyVYSELPSAEEKMKVTVTQITVALSS<LKNIFTLLVF*GLLSFLTW*IAACLFSTSLFGLFYHQYLTVA

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 .00 RPM 5 .92 RPM
bodymap2_adrenal 0 .00 RPM 14 .14 RPM
bodymap2_brain 0 .00 RPM 15 .24 RPM
bodymap2_breast 0 .04 RPM 10 .37 RPM
bodymap2_colon 0 .00 RPM 8 .33 RPM
bodymap2_heart 0 .00 RPM 8 .33 RPM
bodymap2_kidney 0 .00 RPM 22 .48 RPM
bodymap2_liver 0 .00 RPM 8 .75 RPM
bodymap2_lung 0 .00 RPM 8 .49 RPM
bodymap2_lymph_node 0 .00 RPM 12 .35 RPM
bodymap2_ovary 0 .00 RPM 13 .86 RPM
bodymap2_prostate 0 .00 RPM 16 .13 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .38 RPM
bodymap2_testis 0 .00 RPM 15 .23 RPM
bodymap2_thyroid 0 .00 RPM 25 .69 RPM
bodymap2_white_blood_cells 0 .00 RPM 11 .32 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_560 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_560 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_560 retrocopy 5' end.

Lab - click to see more details

retro_hsap_560 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_560 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_419
Gorilla gorilla retro_ggor_506
Parental genes homology:
Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000108571 retrocopy
retro_cjac_2671,
Homo sapiens ENSG00000164180 1 retrocopy
retro_hsap_560 ,
Gorilla gorilla ENSGGOG000000056841 retrocopy
retro_ggor_506,
Macaca mulatta ENSMMUG000000093191 retrocopy
retro_mmul_719,
Nomascus leucogenys ENSNLEG000000136451 retrocopy
retro_nleu_2224,
Pan troglodytes ENSPTRG000000170641 retrocopy
retro_ptro_419,
Rattus norvegicus ENSRNOG000000324141 retrocopy
retro_rnor_1023,
Ictidomys tridecemlineatus ENSSTOG000000111411 retrocopy
retro_itri_1420,
Ictidomys tridecemlineatus ENSSTOG000000278312 retrocopies
retro_itri_1419, retro_itri_1787,

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 = 0.03 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 .03 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 .03 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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