RetrogeneDB ID:

retro_hsap_1370

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:88419501..88421538(+)
Located in intron of:ENSG00000054983
Retrocopy
information
Ensembl ID:ENSG00000259096
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM35A
Ensembl ID:ENSG00000122376
Aliases:FAM35A, FAM35A1, bA163M19.1
Description:family with sequence similarity 35, member A [Source:HGNC Symbol;Acc:28773]


Retrocopy-Parental alignment summary:






>retro_hsap_1370
AAGTCTGAAGCAGCAGTTAGGAAGGTCTCAGACCTTAAAATGTCAACTGATACGGAATTTCTCTGTATAATTACCTCCAG
CCAGGTTGCTTTTTTAGCTCAAAAGAAAGATAAAGGGCGGAGTCCTATAAATAAAGGGAATGTAAACATGGAGACTGAAC
CAAAGGCAAGTTACGGGAAGATAAGAATATCTGAAGAGAATTCCATTCAACTTGATGATTTTACAGAAGCATATGAAAGT
GGACAAAACCAAGCATATTCTCTTGAACATTTTAGTCCTGTTTTTCCTAAAACAGAAAATAGCCACATTCACATAAACTC
TGACAAAGGTCCTGAAGAAAATACAGGATCTCAAGAACTTTTCAGTTCTGAAGATGAACTGCCACCAAATGAGATACGTA
TTGAGTTGTGTAGCTCAGGAATACTGTGTTCCCAACTAAACACCTTCCACAAAAGTGCTATTAAAAGAAGCTGCACCTCT
GAAGATAAAGTGGGCCAGTCTGAAGCTCTATCTAGAGTCCTTCAAGTAGCTAAGAAAATGAAGTTGATTTCTAATGCAGG
AGATTCTGTTGTAGAAATGGATCAGAGGAATGTGTCTGAATTTAAGGGTATTAAAAAAAGTCATTAATAAAAAACTGTGA
TTCTAAAAGCCAGAAGTATGATTGTTTAGTCATGGTGCTATCTCCATGTCATGTGAAGGAAATAAACATAAAATTCGGAC
CAAATTCTGGCTCTAAAGTGCCTTTAGCAACAGTTACAGTAATTGATCAATCAGAAACTAAGAAGGTTTTTCTGTAGAGG
ACTGCAGCATTTTGGGCATATACAGTGTTTCTTGGAGATATAATTTTACTCGCAGATGTTGTTATTCATGAGGACCAATG
GGTTGGCGAGACAGTACTACAATCAACATTTAGCAGTCAGTTATTAAATCTTGGGAGTTATTCATCTATTCAGCCTGAAG
AATATTCCAGTGTAGTTAGTGATGTTGTACTTCAAGACCTACTGGCACAGGTGTCCTCAAAACATTCCTACCTCAGAGAT
CTTCCTCCGAGGCAGCCTCAGAGGGTGAACAGTATAGACTTTATAGAATTGGAGCACCTTCAGCCTGATGTATTAGTCCA
CACAATACTAAGAGTTGTTGATTTCACTATACTGACAGAGGCAGTATACAGTTATAGAGGACAGAAGCAGAAAAAGTTAT
GTTAACAGTGGAACAGGCCCAAGATCAACATTATGTGCTTGTATTATGGAGTCCTGGAGCAGCCTGGTACCCTCAACTGC
AAAGGAAAAAAGGTTATATTTGGGAATTTAAATATCTTTTTGTTCAGCGCAATTACACACTAGAAAACCTAAAATCGCAT
ACAATGCCTTGGTCATCCTGTGAGTGCTTGTTTGATGATGATGTAAGGGCAATTACATTTAAAGCAAAATTTCAAAAAAG
TGCACCTTCCTTTTGGAAGATATCAGACTTAGCAACCCACCTAGAGGATAAATGTTCAGGAGTGGTTCTAATTAAAGCCC
AGATTTCAGAGCTGTCATTTCCTATTACGGCAGCTCAGAAGATAGCTCTAAATGCTCACAGTTCTCTGAAGAGTATTTCT
TTTCTTCTCTTCCCAACATCATATATACTGGCTGCGCAAAATATGGATTGGAACTAGAAACAGATAAGAACAGGATCTAC
AAACAATGTTTTAGCTGCTTGCCATTTACTATGAAGAAAATATACTATAGGCCAGCTTTAATGACTGTAGTTGATGGAAG
ACATGATGTTTACATCCGTGTAGACTCAAAGCTGATAGAGAAGATTCTTCTCAACATTTTTGCAGACTGCCTCAACAGAG
TGATAGTTACTTCCTCAGAGATCACCTATGGGATGGTCATGGCAGACCTGTTACACTCCTTGTCGGCAGTCAGCGCAGAA
CCTTGTGTATCAAAGATTCAGAGCCTTTTTGTGTTAGATGAAAGCAGCTATCCATTACAACAAGATTTCTCCCTCCTGGA
TTTTTATCCTGACACTGTAAAGCATGGAGCCGATGCC

ORF - retro_hsap_1370 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.23 %
Parental protein coverage: 75.22 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalRSEAAVRKVSDLKISTDTEFLSIITSSQVAFLAQKKDKRRSPVNKGNVNMETEPKASYGEIRIPEENSIQ
.SEAAVRKVSDLK.STDTEFL.IITSSQVAFLAQKKDK.RSP.NKGNVNMETEPKASYG.IRI.EENSIQ
RetrocopyKSEAAVRKVSDLKMSTDTEFLCIITSSQVAFLAQKKDKGRSPINKGNVNMETEPKASYGKIRISEENSIQ
ParentalLDGFTEAYESGQNQAYSLELFSPVCPKTENSRIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSG
LD.FTEAYESGQNQAYSLE.FSPV.PKTENS.IHINSDKG.EE.TGSQELFSSEDELPPNEIRIELCSSG
RetrocopyLDDFTEAYESGQNQAYSLEHFSPVFPKTENSHIHINSDKGPEENTGSQELFSSEDELPPNEIRIELCSSG
ParentalILCSQLNTFHKSAIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKSIKKT-SL
ILCSQLNTFHKSAIKRSCTSEDKVGQSEALSRVLQVAKKMKLISN.GDS.VEMD.RNVSEFK.IKK..SL
RetrocopyILCSQLNTFHKSAIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNAGDSVVEMDQRNVSEFKGIKKS<SL
ParentalIKNCDSKSQKYNCLVMVLSPCHVKEINIKFGPNSGSKVPLATVTVIDQSETKKKVFLWRTAAFWAFTVFL
IKNCDSKSQKY.CLVMVLSPCHVKEINIKFGPNSGSKVPLATVTVIDQSET.KKVFL.RTAAFWA.TVFL
RetrocopyIKNCDSKSQKYDCLVMVLSPCHVKEINIKFGPNSGSKVPLATVTVIDQSET-KKVFL*RTAAFWAYTVFL
ParentalGDIILLTDVVIHEDQWIGETVLQSTFSSQLLNLGSYSSIQPEEYSSVVSEVVLQDLLAYVSSKHSYLRDL
GDIILL.DVVIHEDQW.GETVLQSTFSSQLLNLGSYSSIQPEEYSSVVS.VVLQDLLA.VSSKHSYLRDL
RetrocopyGDIILLADVVIHEDQWVGETVLQSTFSSQLLNLGSYSSIQPEEYSSVVSDVVLQDLLAQVSSKHSYLRDL
ParentalPPRQPQRVNSIDFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQK-KVMLTVEQAQDQHYALVLW
PPRQPQRVNSIDF.ELEHLQPDVLVH..LRVVDFTILTEAVYSYRGQKQK.KVMLTVEQAQDQHY.LVLW
RetrocopyPPRQPQRVNSIDFIELEHLQPDVLVHTILRVVDFTILTEAVYSYRGQKQK<KVMLTVEQAQDQHYVLVLW
ParentalGPGAAWYPQLQRKKGYIWEFKYLFVQCNYTLENLELHTTPWSSCECLFDDDIRAITFKAKFQKSAPSFVK
.PGAAWYPQLQRKKGYIWEFKYLFVQ.NYTLENL..HT.PWSSCECLFDDD.RAITFKAKFQKSAPSF.K
RetrocopySPGAAWYPQLQRKKGYIWEFKYLFVQRNYTLENLKSHTMPWSSCECLFDDDVRAITFKAKFQKSAPSFWK
ParentalISDLATHLEDKCSGVVLIKAQISELAFPITASQKIALNAHSSLKSI-FSS-LPNIVYTGCAKCGLELETD
ISDLATHLEDKCSGVVLIKAQISEL.FPITA.QKIALNAHSSLKSI.F.S.LPNI.YTGCAK.GLELETD
RetrocopyISDLATHLEDKCSGVVLIKAQISELSFPITAAQKIALNAHSSLKSI<FFSSLPNIIYTGCAKYGLELETD
ParentalENRIYKQCFSCLPFTMKKIYYRPALMTAIDGRHDVCIRVESKLIEKILLNISADCLNRVIVPSSEITYGM
.NRIYKQCFSCLPFTMKKIYYRPALMT..DGRHDV.IRV.SKLIEKILLNI.ADCLNRVIV.SSEITYGM
RetrocopyKNRIYKQCFSCLPFTMKKIYYRPALMTVVDGRHDVYIRVDSKLIEKILLNIFADCLNRVIVTSSEITYGM
ParentalVVADLFHSLLAVSAEPCVLKIQSLFVLDENSYPLQQDFSLLDFYPDIVKHGANA
V.ADL.HSL.AVSAEPCV.KIQSLFVLDE.SYPLQQDFSLLDFYPD.VKHGA.A
RetrocopyVMADLLHSLSAVSAEPCVSKIQSLFVLDESSYPLQQDFSLLDFYPDTVKHGADA

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 .02 RPM 23 .04 RPM
bodymap2_adrenal 0 .04 RPM 36 .80 RPM
bodymap2_brain 0 .00 RPM 12 .19 RPM
bodymap2_breast 0 .00 RPM 47 .69 RPM
bodymap2_colon 0 .00 RPM 20 .40 RPM
bodymap2_heart 0 .06 RPM 12 .50 RPM
bodymap2_kidney 0 .00 RPM 51 .27 RPM
bodymap2_liver 0 .00 RPM 43 .89 RPM
bodymap2_lung 0 .00 RPM 12 .66 RPM
bodymap2_lymph_node 0 .00 RPM 26 .09 RPM
bodymap2_ovary 0 .00 RPM 38 .80 RPM
bodymap2_prostate 0 .00 RPM 27 .76 RPM
bodymap2_skeletal_muscle 0 .00 RPM 13 .77 RPM
bodymap2_testis 0 .08 RPM 26 .90 RPM
bodymap2_thyroid 0 .00 RPM 53 .39 RPM
bodymap2_white_blood_cells 0 .00 RPM 36 .40 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1370 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1370 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1370 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1370 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1370 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_941
Pongo abelii retro_pabe_1137
Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000000171 retrocopy
retro_dnov_2237,
Homo sapiens ENSG00000122376 1 retrocopy
retro_hsap_1370 ,
Nomascus leucogenys ENSNLEG000000116523 retrocopies
retro_nleu_1073, retro_nleu_2157, retro_nleu_840,
Pongo abelii ENSPPYG000000028281 retrocopy
retro_pabe_1137,
Pan troglodytes ENSPTRG000000024651 retrocopy
retro_ptro_941,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 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 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

The presence of retro_hsap_1370 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1370 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 14:88391508..88423200 100 100 100 100 100 100 99.41 100 99.44 99.46 100 100 100 100

Indel #1, located at the genomic coordinates 14:88391508..88423200.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 99.41 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 99.44 % Finnish in Finland FIN 99.46 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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