RetrogeneDB ID:

retro_hsap_2318

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:132085748..132087386(-)
Located in intron of:ENSG00000115762
Retrocopy
information
Ensembl ID:ENSG00000227817
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARHGAP42
Ensembl ID:ENSG00000165895
Aliases:ARHGAP42, GRAF3
Description:Rho GTPase activating protein 42 [Source:HGNC Symbol;Acc:26545]


Retrocopy-Parental alignment summary:






>retro_hsap_2318
AAAACTTGTATCCGACGAAAGACAGATTCAATTGACAACCACTTCTGCTTCGACATACAAGTAGTTGAAAGGCATGGGAT
CATCACATTACAGGCCTTCTCAGACGCTAATAGGAAACTCTGGCTTGAAGCCATGGATGGGAAGGAAATGATTTATACTC
TGCCTGACATTATAAGCAAGAAAGAAGAAAGGTATTTGAATGAAGCAGGGTTCAATTTTGTGAGAAACTGCATTCAAGCT
GTGGAAACAAGCGGTATCACCGTTTTAGGCCTCTACTGAATAGGAGGAGTGAACTCCAAAGTTCAAAAACTTGTGAATAT
CATATTTTCTCCTAAATCCCCTCCTGATATTGATATTGAACTGTGGGACAATAAGACAATGAGTGGGCTGAAAAACTACC
TCAGGTGCTTTGCAGCACCACTGATGACTTACAAGTTACACAAAGATTTGTATCATTGCTGTTAAATCTGATGACCAAAA
CTACAGGGTGGAGGCTGTACATGCATTGGTGTGCAAATTGCCAGAGAAAAACAGAGAGATGCTGGACATCTTAATAAAAC
ATCTGGTCAAAGTATCACTGCACAGCCAACAAAATCTCATGACTGTCTCAAATCTTGGTGTCATATTTCTCCCAACTCTA
ATGAGAGCACAAGAATAAACTGTAGCTGCTATGGTGAATATTAAATTTCAGAATATTGTGTTAGAAATTCTTACAGAGCA
CGATGAAACGATTTTTCATACTGCTCCAGACCCAAGCATTCCTCTTCCTCAGCCTCAGTCTCGATCTGGATCCCAAAGGA
CACGAGCAATCTGCCTCTCTACAGGCTCTAGGAAGCCCAGAGGGACGTGTACTCCATACCTGGCTGAACCTGACAGTGAC
TCCTATAGCAGCAGCCCAGACAGCACCCCCATGGGGAGCATCAAGTCACTCTCTTCTCTTTCCTCGGAACAAAATAGCAC
TACAAAGTCAGCTTCCTGCCAGCCCAGGGAGAAATCTGGAGGGATTCCTTGGATTGCAACCCTTTCATCTTCCCATGGAC
AGAAAAGCCTTGGTCTCTGGACAACCAGTCCTGAATCAAGTTCTAGAGAAGATGCAACCAAGACAGATGCAGAATCAGAT
TGCCAGAGTGCTGCTTCGGTCACTAGCCCAGGGGATGTTCCCCCACCCATAGACCTAGTCAAGAAAGGGCCTTATGGACT
TTCAGGACTGAAAAGAGCTTCTGCTTCTTCTCTCAGATCCATCTCTGCAGCTGAAGGAAACACCAGCTACAGTGGATCTA
TTCAAAGCTTAACTTCTGTAGGTTCCAAGAAGACACCCAAAGCTTCAAACCCAGACCTGCCTCCAAAAATGTGCAGGAGG
TTAAGACTAGACACCACTGCAAGCAATAGCTATCAGCGTACTGGCTCAGTAGTGGCAGCAAAAGCTCAACTGTTTGAAAA
TGTTGGTTCACCTAAGCCAGTTTCTTCTGGGCACCAAGCCAAAGCCATGTACTCCTGTAAAGCAGAGCACAGCATGAGTT
TTCCTTCCCACAAGGAGCGATATTTTCCAGCGTGGACCCATCAGTGGAACCAGGATGGTTAAAGGCAACTTATGAAGGCA
AAACGGGACTAGTTCCAGAAAATTATGTTGTCTTCCTC

ORF - retro_hsap_2318 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.22 %
Parental protein coverage: 62.93 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKSCIRRKTDSIDKRFCFDIEVVERHGIITLQAFSEANRKLWLEAMDGKEPIYTLPAIISKKEEMYLNEAG
K.CIRRKTDSID..FCFDI.VVERHGIITLQAFS.ANRKLWLEAMDGKE.IYTLP.IISKKEE.YLNEAG
RetrocopyKTCIRRKTDSIDNHFCFDIQVVERHGIITLQAFSDANRKLWLEAMDGKEMIYTLPDIISKKEERYLNEAG
ParentalFNFVRKCIQAVETRGITILGLYRIGGVNSKVQKLMNTTFSPKSPPDIDIDIELWDNKTITSGLKNYLRCL
FNFVR.CIQAVET.GIT.LGLY.IGGVNSKVQKL.N..FSPKSPPDIDI..ELWDNKT..SGLKNYLRC.
RetrocopyFNFVRNCIQAVETSGITVLGLY*IGGVNSKVQKLVNIIFSPKSPPDIDI--ELWDNKTM-SGLKNYLRCF
ParentalAEPLMTYKLHKDF-IIAVKSDDQNYRVEAVHALVHKLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLG
A.PLMTYKLHKD..IIAVKSDDQNYRVEAVHALV.KLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLG
RetrocopyAAPLMTYKLHKDL>IIAVKSDDQNYRVEAVHALVCKLPEKNREMLDILIKHLVKVSLHSQQNLMTVSNLG
ParentalVIFGPTLMRAQEETVAAMMNIKFQNIVVEILIEHYEKIFHTAPDPSIPLPQPQSRSGSRRTRAICLSTGS
VIF.PTLMRAQE.TVAAM.NIKFQNIV.EIL.EH.E.IFHTAPDPSIPLPQPQSRSGS.RTRAICLSTGS
RetrocopyVIFLPTLMRAQE*TVAAMVNIKFQNIVLEILTEHDETIFHTAPDPSIPLPQPQSRSGSQRTRAICLSTGS
ParentalRKPRGRYTPCLAEPDSDSYSSSPDSTPMGSIESLSSHSSEQNSTTKSASCQPREKSGGIPWIATPSSSNG
RKPRG..TP.LAEPDSDSYSSSPDSTPMGSI.SLSS.SSEQNSTTKSASCQPREKSGGIPWIAT.SSS.G
RetrocopyRKPRGTCTPYLAEPDSDSYSSSPDSTPMGSIKSLSSLSSEQNSTTKSASCQPREKSGGIPWIATLSSSHG
ParentalQKSLGLWTTSPESSSREDATKTDAESDCQSVASVTSPGDVSPPIDLVKKEPYGLSGLKRASASSLRSISA
QKSLGLWTTSPESSSREDATKTDAESDCQS.ASVTSPGDV.PPIDLVKK.PYGLSGLKRASASSLRSISA
RetrocopyQKSLGLWTTSPESSSREDATKTDAESDCQSAASVTSPGDVPPPIDLVKKGPYGLSGLKRASASSLRSISA
ParentalAEGNKSYSGSIQSLTSVGSKETPKASPNPDLPPKMCRRLRLDTASSNGYQRPGSVVAAKAQLFENVGSPK
AEGN.SYSGSIQSLTSVGSK.TPKAS.NPDLPPKMCRRLRLDT..SN.YQR.GSVVAAKAQLFENVGSPK
RetrocopyAEGNTSYSGSIQSLTSVGSKKTPKAS-NPDLPPKMCRRLRLDTTASNSYQRTGSVVAAKAQLFENVGSPK
ParentalPVSSGRQAKAMYSCKAEHS-HELSFPQGAIFSNVYPSVEPGWLKATYEGKTGLVPENYVVFL
PVSSG.QAKAMYSCKAEHS.HE.SFPQGAIFS.V.PSVEPGWLKATYEGKTGLVPENYVVFL
RetrocopyPVSSGHQAKAMYSCKAEHS<HEFSFPQGAIFSSVDPSVEPGWLKATYEGKTGLVPENYVVFL

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 25 .46 RPM
bodymap2_adrenal 0 .00 RPM 17 .42 RPM
bodymap2_brain 0 .02 RPM 9 .33 RPM
bodymap2_breast 0 .00 RPM 23 .48 RPM
bodymap2_colon 0 .00 RPM 13 .59 RPM
bodymap2_heart 0 .00 RPM 11 .82 RPM
bodymap2_kidney 0 .00 RPM 16 .71 RPM
bodymap2_liver 0 .00 RPM 10 .20 RPM
bodymap2_lung 0 .00 RPM 35 .09 RPM
bodymap2_lymph_node 0 .00 RPM 17 .27 RPM
bodymap2_ovary 0 .00 RPM 10 .26 RPM
bodymap2_prostate 0 .00 RPM 8 .92 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .98 RPM
bodymap2_testis 0 .00 RPM 16 .68 RPM
bodymap2_thyroid 0 .00 RPM 22 .86 RPM
bodymap2_white_blood_cells 0 .00 RPM 1 .75 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2318 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2318 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2318 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2318 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2318 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG000000058291 retrocopy
retro_ecab_997,
Homo sapiens ENSG00000165895 2 retrocopies
retro_hsap_2156, retro_hsap_2318 ,
Gorilla gorilla ENSGGOG000000113972 retrocopies
retro_ggor_1714, retro_ggor_1758,
Pongo abelii ENSPPYG000000037991 retrocopy
retro_pabe_2095,
Pan troglodytes ENSPTRG000000042044 retrocopies
retro_ptro_1641, retro_ptro_1692, retro_ptro_3083, retro_ptro_892,

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 = 0.05 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 .05 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 .03 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:

The presence of retro_hsap_2318 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2318 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. 2:132087258..132097000 97.54 93.75 90.72 100 100 100 100 100 99.44 100 100 100 99.48 100

Indel #1, located at the genomic coordinates 2:132087258..132097000.

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 97.54 % Yoruba in Ibadan,Nigeria YRI 93.75 % Luhya in Webuye,Kenya LWK 90.72 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 99.44 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 99.48 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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