RetrogeneDB ID:

retro_sscr_252

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:10:77826850..77827930(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:POU5F1
Ensembl ID:ENSSSCG00000001393
Aliases:POU5F1, OCT3, OCT4, Oct-4
Description:Sus scrofa POU class 5 homeobox 1 (POU5F1), mRNA. [Source:RefSeq mRNA;Acc:NM_001113060]


Retrocopy-Parental alignment summary:






>retro_sscr_252
GCTGAACACCTGGCTTCCAACCCTGCCTTCTTTTCCTTGCCATGCAGTGCAGATGATGGGCTGGGAGGGCCAGAGCCTGG
CTGGGATGATCCTCAGACATGGGTCAGCTTCCAAGGAACTCCCAAGCAGTCAGGGATTAGGCCAGGGGGATGGGCTGGGC
ACCAAGGTGTGAGGGCTTCACAATCCCCCACCACCATCTTATGGCTTCTGAAGGGGTATGGCCTCCTGCACACCTCAGGT
CAGAGTGGGGCTTGTGCCTCAGCACAGCCTGGAGACTCCTCAGCATAAGGCAAGATAGGAGCTTGGGTGGGGAGCAACTC
CAAGAGGCCCACCCCCATCCCTGTGCCACCTGCTGGTGCTGCAAAGCTGGACAAAGAGAAGCTGGAACCCAACCTCCCCA
AGGAGTCCCAGGACATAAAATCACTTTAGAATGACATCAAACAATCTGCCAAGCTCCTAAAGCAGAAGAGGATCACCCTG
ATATATACCCAGGCTGATGTGGGGCTCAACTTGTGGGTTCTCTTTGGGAACACATTCAGCCAAATTACCATCCACCATTT
TGAGGCTCTGCAGCTCAGTTTCACCAACATATCTAAGCTTCGGACCTCGCTACAGAAGTGGGTGGAGGAATCTTACAACA
AGGAGAATCTACAGGAGATATACAAAGCAAAGACTCTTCTGCATGCCTGGAAGGGAAAGAAGACAAGTATGGAGAACCCA
GTGAGGGGCAACCTGGAGAGCATGTTCCTGTAGGGCCTGAAACCCACCCTGCAGCATATCAGCCACATTGTCCAGCTGCT
TGGACTTGAGAAGAATGTGGTCTGAGTATGGTTCTCCAAACTTTGCCAGAAGGGCAAAGGATCAAGCTGTGGCTCTTCAC
AAGGAGAGTGTGTTGAGGCTGCTGGGTCTCCTTTCCCAGAGGGACCAGTATCCTTTCCTCTGGTTACAGAGCCCCATCTT
GGTACCCCAGGCAGTAGGGGCCCTCACTTCACCATGCTGTCCTCCTAGATCCCTTTCCCTAAGGGTCAGTCCTTTTCCTC
AATGTCTGTCATCACTCTGGGCTCTCCCATACATTCAAAT

ORF - retro_sscr_252 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.39 %
Parental protein coverage: 99.72 %
Number of stop codons detected: 6
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGSGIGPGV-GPGAEVWGLPACPPP-YDF
A.HLAS..AF...P....DG.GGPEPGW.DP.TW.SFQG.P..SGI.PG..G.G..V.GL...PPP.Y.F
RetrocopyAEHLASNPAFFSLPCSADDGLGGPEPGWDDPQTWVSFQGTPKQSGIRPGG>GLGTKV*GLHNPPPPSYGF
ParentalCGGMAYCAPQVGVGLVPQGGLETPQPE-GEAGAGVESNSEGASPEPCAAPAGAAKLDKEKLEPN-PEESQ
..GMA.C.PQV.VGLVPQ..LETPQ...G..GA.V.SNS....P.P...PAGAAKLDKEKLEPN.P.ESQ
Retrocopy*RGMASCTPQVRVGLVPQHSLETPQHK<GKIGAWVGSNSKRPTPIP-VPPAGAAKLDKEKLEPNLPKESQ
ParentalDIKALQKDLEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKW
DIK.L..D..Q.AKLLKQKRITL.YTQADVGL.L.VLFG..FSQ.TI..FEALQLSF.N..KLR..LQKW
RetrocopyDIKSL*NDIKQSAKLLKQKRITLIYTQADVGLNLWVLFGNTFSQITIHHFEALQLSFTNISKLRTSLQKW
ParentalVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLESMFLQCPKPTLQQISHIAQQLGLEKDVVRVW
VEE..N.ENLQEI.KA.TL..A.K.K.TS.EN.VRGNLESMFL...KPTLQ.ISHI.Q.LGLEK.VV.VW
RetrocopyVEESYNKENLQEIYKAKTLLHAWKGKKTSMENPVRGNLESMFL*GLKPTLQHISHIVQLLGLEKNVV*VW
ParentalFCNRRQKGKRSSSDYSQREDFEAAGSPFPGGPVSFPLAPGPHFGTPGYGGPHFTTLYSSVPFPEGEAFPS
F....QKGK.SS...SQ.E..EAAGSPFP.GPVSFPL...PH.GTPG..GPHFT.L.S..PFP.G..F.S
RetrocopyFSKLCQKGKGSSCGSSQGECVEAAGSPFPEGPVSFPLVTEPHLGTPGSRGPHFTMLSS*IPFPKGQSFSS
ParentalVSVTPLGSPMHSN
.SV..LGSP.HSN
RetrocopyMSVITLGSPIHSN

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
SRP014902_placenta 0 .00 RPM 0 .27 RPM
SRP014902_testis 0 .00 RPM 0 .85 RPM
SRP018288_heart 0 .00 RPM 0 .03 RPM
SRP018288_kidney 0 .00 RPM 0 .00 RPM
SRP018288_liver 0 .00 RPM 0 .00 RPM
SRP018288_lung 0 .00 RPM 0 .00 RPM
SRP018856_adipose 0 .00 RPM 0 .02 RPM
SRP035408_brain 0 .00 RPM 0 .00 RPM
SRP035408_liver 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_252 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_252 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_252 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 63 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000103773 retrocopies
retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus ENSBTAG000000211112 retrocopies
retro_btau_1576, retro_btau_951,
Canis familiaris ENSCAFG000000004851 retrocopy
retro_cfam_1538,
Callithrix jacchus ENSCJAG000000197891 retrocopy
retro_cjac_123,
Dipodomys ordii ENSDORG000000095491 retrocopy
retro_dord_65,
Equus caballus ENSECAG000000089671 retrocopy
retro_ecab_301,
Erinaceus europaeus ENSEEUG000000153572 retrocopies
retro_eeur_196, retro_eeur_558,
Felis catus ENSFCAG000000010783 retrocopies
retro_fcat_1372, retro_fcat_1422, retro_fcat_275,
Gorilla gorilla ENSGGOG000000276623 retrocopies
retro_ggor_2275, retro_ggor_295, retro_ggor_852,
Macropus eugenii ENSMEUG000000132213 retrocopies
retro_meug_1146, retro_meug_1475, retro_meug_692,
Microcebus murinus ENSMICG000000015111 retrocopy
retro_mmur_1423,
Myotis lucifugus ENSMLUG000000110283 retrocopies
retro_mluc_1465, retro_mluc_2382, retro_mluc_515,
Mustela putorius furoENSMPUG000000012022 retrocopies
retro_mputfur_253, retro_mputfur_96,
Mus musculus ENSMUSG000000244062 retrocopies
retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus ENSOCUG000000171603 retrocopies
retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Otolemur garnettii ENSOGAG000000006213 retrocopies
retro_ogar_1406, retro_ogar_1436, retro_ogar_2229,
Ochotona princeps ENSOPRG000000039262 retrocopies
retro_opri_1213, retro_opri_556,
Pongo abelii ENSPPYG000000172103 retrocopies
retro_pabe_2761, retro_pabe_3294, retro_pabe_898,
Pan troglodytes ENSPTRG000000179535 retrocopies
retro_ptro_1798, retro_ptro_204, retro_ptro_2132, retro_ptro_2721, retro_ptro_733,
Pteropus vampyrus ENSPVAG000000073342 retrocopies
retro_pvam_724, retro_pvam_74,
Rattus norvegicus ENSRNOG000000464874 retrocopies
retro_rnor_1474, retro_rnor_2186, retro_rnor_2968, retro_rnor_921,
Sus scrofa ENSSSCG00000001393 2 retrocopies
retro_sscr_252 , retro_sscr_678,
Ictidomys tridecemlineatus ENSSTOG000000261033 retrocopies
retro_itri_1076, retro_itri_1705, retro_itri_951,
Tupaia belangeri ENSTBEG000000130444 retrocopies
retro_tbel_3628, retro_tbel_3718, retro_tbel_3779, retro_tbel_4614,
Tarsius syrichta ENSTSYG000000073404 retrocopies
retro_tsyr_1508, retro_tsyr_1630, retro_tsyr_814, retro_tsyr_817,


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