RetrogeneDB ID:

retro_hsap_565

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:45301894..45303421(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227395
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF2A
Ensembl ID:ENSG00000144895
Aliases:EIF2A, EIF-2A, MST089, MSTP004, MSTP089
Description:eukaryotic translation initiation factor 2A, 65kDa [Source:HGNC Symbol;Acc:3254]


Retrocopy-Parental alignment summary:






>retro_hsap_565
GGATCAGAAGGACTCTGTGTGGTGAATGCACCACCATGTTTTGCAGAAAGCATAGTGTTTCCAAGGAAATCTCAGGAAAA
TTACAAAATCTGTAACTTTAGCAACAGTTGGAGCTTCATTTGCTGGGGCAAAGGAAAAAAATTATAAATATTATCAGTGT
CACTAACATGAGTTTACTACACCTCTTCCACCTCCAAAGGCACTTTTTTCTGAATTCTTACCAAAAACCCATGTCCTGGT
AATACAGCAGCCTTACACTTCCCTACACATGGCACTCCTGGGAGACTCAACCTGCAACTCCATCGTGTGAGAGTGGGATG
TGCTTGAAGTCTTTCATCAAGGAAAAAATGTAAATTGGTATCCATCTGGTCAGATGATGAAACTGTTTTGTGTCCAAAAT
GTTAACAATAAAGTTCACTTCTTTGTAAACGATGATTTTATAAAATTGCAAGTAAATTGTCTTTGCAGAAAATTAATTGT
GGGTTATCACTTGGACTCCAGTCACACAAGGGGGCTGTCTATGTTTCAGGGAGTGAGGGTGTACTTTCATTTGTTGTATT
ATACTCATACCCCAACTTTTTTGGACCTCATGCAGCTTTAGCCAACAGCAGTTTCTCTAAGCCGATGAGGTTACAACGCT
GTGGAATGAAAAAGCCACTGCTGGCTTGTAATAGCGAGAACAGATGTTGACAAGAGAAGAACTTCCTGCTATGGGGAACA
AAGGCTGCATTGCACTGCAACAAATGGAGAAAGTGCTGTCATTTGTTCAATTACTAAAACATAGCCCCATTTATGATATA
ATTTGGAATTCTGGTTCTACTGAGTTTTATGCTATTTATGGTTTTATGCCTGCCAAAGCTATGATTTTCAACTTGAAATG
TGATCTTGTGTTTGACCTTGGAACTGGTGCTCTAAGGCAGCCTATTCGGTCCTTGTGGCCATATATTAATACTAACTGGA
TTTGGAAATCTGAGGAACAAACGTGAGTGTGGGATATTAAAAGCTACAAACTTATTTCCAAACAAGTATCCTCTGATCAT
ACATATTTTGCTAGGTACCTAGATGGGAGCACCTTTTACTATCACACATGCTCCCAGGTTGTGTGTTAATAATGGATACA
AGCTTTGACATTATACCAGCCCTATCCTGCATGAGTAAGATGTGTCACCAAATGTAGAAATATGGCAGGCTTCTTGGCAG
ACATTTCTGGATGAACTATTTCCAGCAAAAGCAGTAACTTATCAAGCAGTTCCAAGTGAAGTACCCAACTAGGAACCTAA
ATTTGCAATGACTGATAGACTCCCAGCTTTAAGAAATAAAACAATCACCAATTCTAAGCTGTATGAAGAGAAATCACCCC
AGAATAAGAAATCCCAACCAGGAAATGATAAACCATTAACAAAAGCAGCCCTGAAAAATCAAAGGAAATATAAAGCTAAG
AAAGCTACAAAGCAGGAAGTAAGAAGTGACAAGAGTCCAGATTTGACACCTACCCCTGTCCCCCAGAGCACACCCTGAAA
TACAGTG

ORF - retro_hsap_565 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.72 %
Parental protein coverage: 87.52 %
Number of stop codons detected: 5
Number of frameshifts detected 16


Retrocopy - Parental Gene Alignment:

ParentalGSEGLYMVNGPPHFTESTVFPRESGKNCKVCIFSKDGTLFAW-GNGEKV-NIISVTNKGLLHSFDLL-KA
GSEGL..VN.PP.F.ES.VFPR.S..N.K.C.FS.......W.G...K..NIISVTN..LLH.F.L..KA
RetrocopyGSEGLCVVNAPPCFAESIVFPRKSQENYKICNFSNSWSFICW<GQRKKIINIISVTNMSLLHLFHLQ<KA
ParentalVCLEFSPKNTVLATWQPYTT-SKDGTAGIPNLQLYDVK-TGTCLKSFIQKKM-QNWCPS-WSEDETL-CA
...EF.PK..VL...QPYT.....GT.G..NLQL..V...G.CLKSFI..KM..NW.PS.WS.DET..C.
RetrocopyLFSEFLPKTHVLVIQQPYTS<PTHGTPGRLNLQLHRVR<SGMCLKSFIKEKM<VNWYPS<WSDDETV>CV
ParentalRNVNNEVHFFENNNF-NTIANKLHLQKINDFVLSPGPQPYKVAVYVPGSKGAPSFVRLYQYPNFAGPHAA
.NVNN.VHFF.N..F...IA.KL.LQKIN...LS.G.Q..K.AVYV.GS.G..SFV.LY.YPNF.GPHAA
RetrocopyQNVNNKVHFFVNDDF<YKIASKLSLQKIN-CGLSLGLQSHKGAVYVSGSEGVLSFVVLYSYPNFFGPHAA
ParentalLANKSFFK-ADKVTMLWNKKATA-VLVIASTDVDKTGASYYGEQTLHYIATNGESAVV-QLPKNGP-IYD
LAN.SF.K.AD.VT.LWN.KATA..LVIA.TDVDK...S.YGEQ.LH..ATNGESAV.....K..P.IYD
RetrocopyLANSSFSK<ADEVTTLWNEKATA<WLVIARTDVDKRRTSCYGEQRLHCTATNGESAVICSITKT*P>IYD
ParentalVVWNSSSTEFCAVYGFMPAKATIFNLKCDPVFDFGTGP-RNAAY-YSPHGHILVLAGFGNLRGQME-VWD
..WNS.STEF.A.YGFMPAKA.IFNLKCD.VFD.GTG....AAY...P.GHIL.L.GFGNLR...E.VWD
RetrocopyIIWNSGSTEFYAIYGFMPAKAMIFNLKCDLVFDLGTGA<SKAAY<FGPCGHILILTGFGNLRNKRE<VWD
ParentalVKNYKLISKPVASDSTYFAWCPDG-EHIL-TATCAPRLRVNNGYKIWHYTGSILHKYDVPSNAELWQVSW
.K.YKLISK.V.SD.TYFA...DG.EH.L.T.T.APRL.VNNGYK..HYT..ILH..DV..N.E.WQ.SW
RetrocopyIKSYKLISKQVSSDHTYFARYLDG<EHLL<TITHAPRLCVNNGYKL*HYTSPILHE*DVSPNVEIWQASW
ParentalQPFLDGIFPAKTITYQAVPSEVPNEEPKVATAYRPPALRNKPITNSKLHEEEPPQNMKPQSGNDKPLSKT
Q.FLD..FPAK..TYQAVPSEVPN.EPK.A...R.PALRNK.ITNSKL.EE..PQN.K.Q.GNDKPL.K.
RetrocopyQTFLDELFPAKAVTYQAVPSEVPN*EPKFAMTDRLPALRNKTITNSKLYEEKSPQNKKSQPGNDKPLTKA
ParentalALKNQRKHEAKKAAKQEARSDKSPDLAPTPAPQSTPRNTV
ALKNQRK..AKKA.KQE.RSDKSPDL.PTP.PQSTP.NTV
RetrocopyALKNQRKYKAKKATKQEVRSDKSPDLTPTPVPQSTP*NTV

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 .04 RPM 101 .42 RPM
bodymap2_adrenal 0 .00 RPM 102 .80 RPM
bodymap2_brain 0 .12 RPM 78 .43 RPM
bodymap2_breast 0 .00 RPM 70 .16 RPM
bodymap2_colon 0 .00 RPM 137 .63 RPM
bodymap2_heart 0 .00 RPM 82 .61 RPM
bodymap2_kidney 0 .00 RPM 79 .72 RPM
bodymap2_liver 0 .00 RPM 64 .77 RPM
bodymap2_lung 0 .00 RPM 78 .53 RPM
bodymap2_lymph_node 0 .00 RPM 100 .14 RPM
bodymap2_ovary 0 .02 RPM 111 .05 RPM
bodymap2_prostate 0 .00 RPM 176 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 154 .96 RPM
bodymap2_testis 0 .00 RPM 89 .61 RPM
bodymap2_thyroid 0 .00 RPM 120 .78 RPM
bodymap2_white_blood_cells 0 .00 RPM 136 .91 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_565 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_565 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_565 retrocopy 5' end.

Lab - click to see more details

retro_hsap_565 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_565 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_423
Gorilla gorilla retro_ggor_509
Pongo abelii retro_pabe_517
Macaca mulatta retro_mmul_2395
Parental genes homology:
Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000011991 retrocopy
retro_cjac_968,
Dasypus novemcinctus ENSDNOG000000140021 retrocopy
retro_dnov_1148,
Homo sapiens ENSG00000144895 1 retrocopy
retro_hsap_565 ,
Gorilla gorilla ENSGGOG000000153911 retrocopy
retro_ggor_509,
Loxodonta africana ENSLAFG000000037671 retrocopy
retro_lafr_502,
Macaca mulatta ENSMMUG000000176961 retrocopy
retro_mmul_2395,
Nomascus leucogenys ENSNLEG000000032191 retrocopy
retro_nleu_2213,
Oryctolagus cuniculus ENSOCUG000000160953 retrocopies
retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,
Pongo abelii ENSPPYG000000296362 retrocopies
retro_pabe_517, retro_pabe_652,
Pan troglodytes ENSPTRG000000155281 retrocopy
retro_ptro_423,
Ictidomys tridecemlineatus ENSSTOG000000033741 retrocopy
retro_itri_1706,

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 .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:

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





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