RetrogeneDB ID:

retro_hsap_3054

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:78879156..78879930(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248926
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SRSF10
Ensembl ID:ENSG00000188529
Aliases:SRSF10, FUSIP1, FUSIP2, NSSR, SFRS13, SFRS13A, SRp38, SRrp40, TASR, TASR1, TASR2
Description:serine/arginine-rich splicing factor 10 [Source:HGNC Symbol;Acc:16713]


Retrocopy-Parental alignment summary:






>retro_hsap_3054
TCCAGCTACCTGCGTCCTCCAAGGTGCCTCTGTTCATCAGGAATGGAGCCAGTAACAGCAGGTTCAAAGATTTATGGCAT
GAATTTGGTCATTATGATCCTATAGTTGATGTGTATGTTCCACTTGATTTCTACACTCACTGTCCAAGAGGAGTTGCTTA
TGTTCAATTGGAAGATGTTCGTGATGCTGAAGATGCTTTACATAATTTGGACAGAAAGTGGATTTGTGGATGTCAAATGG
AAACAGTTTGCACAGGGGGATTGGAAGACCCCAAATCAGATGAAAGCAAAGGAAGGTAGGAGTGTGTACAGTTCTTCACG
CTATGATTATGACAGATATAGATGTTCTAGAAGCCAAAGTTATGAAAGAAGATCAAGAAGTCGGTCTTTTGCTTACATCT
ATAGAAGATCTTGTAGTCCTAGAAAGAGTGGATGGACTGGAAGACCATGGTGTAGCAGAAGCCATTCCAGCAATGATAGA
GTCAAACACTGAAATCAGTCTTTTTCAAGATCTAAATCCAATTCAAGATCAAGGTCCAAGTCCCAGCCCAAGAAAGAAAT
GAAGGCTAAATCGTGTTCTAGGTCTGCATCGCATGCCAAAACTAGAGGCACCTCTAAAACAGATTCCAAAACATATTACA
AGTCTTGCTCAAGACATAAAAAGGAATCAAGGAAAAAAGAACCGCCTTGTTCCAAATCCCAGTCAAGGTCACAGTCTAGG
CCTAGGTCAAAATCTAGATCAAGATCTTGGACTAGTCCTAAATCCAGTGGCTAC

ORF - retro_hsap_3054 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.05 %
Parental protein coverage: 99.62 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalSRYLRPPN-TSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN
S.YLRPP....LF.RN.A...R..DL..EFG.Y.PIVDVYVPLDFYT..PRG.AYVQ.EDVRDAEDALHN
RetrocopySSYLRPPR<VPLFIRNGASNSRFKDLWHEFGHYDPIVDVYVPLDFYTHCPRGVAYVQLEDVRDAEDALHN
ParentalLDRKWICGRQIEIQFAQGDRKTPNQMKAK-EGRNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFDYNYR
LDRKWICG.Q.E.....G....P.....K.EGR.VYSSSRY.DYDRYR.SRS.SYE.RRSRSRSF.Y.YR
RetrocopyLDRKWICGCQME-TVCTGGLEDPKSDESK>EGRSVYSSSRY-DYDRYRCSRSQSYE-RRSRSRSFAYIYR
ParentalRSYSPRNSRPTGRPRRSRSHSDNDRFKHRNRSFSRSKSNSRSRSKSQPKKEMKAKSRSRSASHTKTRGTS
RS.SPR.S..TGRP..SRSHS.NDR.KH.N.SFSRSKSNSRSRSKSQPKKEMKAKS.SRSASH.KTRGTS
RetrocopyRSCSPRKSGWTGRPWCSRSHSSNDRVKH*NQSFSRSKSNSRSRSKSQPKKEMKAKSCSRSASHAKTRGTS
ParentalKTDSKTHYKSGSRYEKESRKKEPPRSKSQSRSQSRSRSKSRSRSWTSPKSSGH
KTDSKT.YKS.SR..KESRKKEPP.SKSQSRSQSR.RSKSRSRSWTSPKSSG.
RetrocopyKTDSKTYYKSCSRHKKESRKKEPPCSKSQSRSQSRPRSKSRSRSWTSPKSSGY

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 2 .72 RPM
bodymap2_adrenal 0 .04 RPM 6 .24 RPM
bodymap2_brain 0 .00 RPM 2 .30 RPM
bodymap2_breast 0 .00 RPM 2 .08 RPM
bodymap2_colon 0 .00 RPM 3 .58 RPM
bodymap2_heart 0 .00 RPM 2 .38 RPM
bodymap2_kidney 0 .00 RPM 4 .24 RPM
bodymap2_liver 0 .00 RPM 0 .82 RPM
bodymap2_lung 0 .00 RPM 2 .14 RPM
bodymap2_lymph_node 0 .00 RPM 3 .12 RPM
bodymap2_ovary 0 .06 RPM 8 .21 RPM
bodymap2_prostate 0 .00 RPM 5 .09 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .76 RPM
bodymap2_testis 0 .00 RPM 4 .96 RPM
bodymap2_thyroid 0 .08 RPM 5 .95 RPM
bodymap2_white_blood_cells 0 .00 RPM 2 .24 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3054 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3054 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3054 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3054 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3054 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2529
Callithrix jacchus retro_cjac_2176
Parental genes homology:
Parental genes homology involve 25 parental genes, and 62 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098692 retrocopies
retro_amel_1810, retro_amel_355,
Bos taurus ENSBTAG000000080721 retrocopy
retro_btau_759,
Choloepus hoffmanni ENSCHOG000000048361 retrocopy
retro_chof_7,
Callithrix jacchus ENSCJAG000000208839 retrocopies
retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus ENSCPOG000000245331 retrocopy
retro_cpor_1098,
Dasypus novemcinctus ENSDNOG000000086993 retrocopies
retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Dipodomys ordii ENSDORG000000091361 retrocopy
retro_dord_667,
Erinaceus europaeus ENSEEUG000000142861 retrocopy
retro_eeur_522,
Homo sapiens ENSG00000188529 5 retrocopies
retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054 , retro_hsap_4295,
Gorilla gorilla ENSGGOG000000003924 retrocopies
retro_ggor_1044, retro_ggor_1411, retro_ggor_1522, retro_ggor_2870,
Loxodonta africana ENSLAFG000000269051 retrocopy
retro_lafr_148,
Myotis lucifugus ENSMLUG000000285201 retrocopy
retro_mluc_89,
Mustela putorius furoENSMPUG000000158451 retrocopy
retro_mputfur_353,
Mus musculus ENSMUSG000000286765 retrocopies
retro_mmus_1081, retro_mmus_1311, retro_mmus_1814, retro_mmus_3480, retro_mmus_982,
Nomascus leucogenys ENSNLEG000000131803 retrocopies
retro_nleu_1647, retro_nleu_1825, retro_nleu_202,
Oryctolagus cuniculus ENSOCUG000000293261 retrocopy
retro_ocun_717,
Otolemur garnettii ENSOGAG000000153742 retrocopies
retro_ogar_2650, retro_ogar_2987,
Ochotona princeps ENSOPRG000000186133 retrocopies
retro_opri_1067, retro_opri_295, retro_opri_916,
Pongo abelii ENSPPYG000000017264 retrocopies
retro_pabe_1115, retro_pabe_1601, retro_pabe_1796, retro_pabe_2529,
Pan troglodytes ENSPTRG000000242344 retrocopies
retro_ptro_1295, retro_ptro_1413, retro_ptro_1986, retro_ptro_918,
Rattus norvegicus ENSRNOG000000079923 retrocopies
retro_rnor_1657, retro_rnor_2800, retro_rnor_2829,
Sus scrofa ENSSSCG000000216152 retrocopies
retro_sscr_528, retro_sscr_554,
Ictidomys tridecemlineatus ENSSTOG000000009561 retrocopy
retro_itri_1333,
Tupaia belangeri ENSTBEG000000177161 retrocopy
retro_tbel_4154,
Tursiops truncatus ENSTTRG000000161502 retrocopies
retro_ttru_1098, retro_ttru_695,

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 .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 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 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 .05 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 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 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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