RetrogeneDB ID:

retro_sscr_621

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:2:57842708..57843438(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA3
Ensembl ID:ENSSSCG00000015988
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]


Retrocopy-Parental alignment summary:






>retro_sscr_621
GTGGAGGTAAAACCACCGCCTGGTCACCCCCAGCTGGACTCCAGCCATTGCCGCCACTGCAGTAGGGCGGGTGGGGGGTA
GGAGGGCCATGATCCAAAGGAACCAAAGCAATTGAGAAAACTGTTTATTGGTGGTCTGAACTTTGAAACTACAGATGATA
GTTTAAGAGAACATTTTGAGAAATGGGGAACACTTACAGATTGTGTGGTGATGAGAGACCCCCAAACAAAATGTTCCAGG
GGATTTGGTTTTGTGACTTATTCTTATGTTGAAGAGGTGGATGCAGTAATGTGTGCTGGACCACATAAGGTTGATGGGCA
GGTAGTGGAACCAAAGAGAGCTGTTTCTAGAGAGGATTCTGTAAAGCCTGGTGCCCATCTAACAGTGAAGAAAATTTTGT
TGGTGGTATTAAAGATACAGAAGAATACAATTTGAGAGACTACTTTGAAAAGTAGGGCAAAATTGAAACCATAGAAGTTA
TGGAAGACAGGCAGAGTAGGAAAAAGAGAGGATTTGCTTTTGTAACTTGTGATGATCATGATACAGTTTTTAAAACTGTT
CAGAAATACTCACACTATAAATGGGCATAACTTGTGAAGTGAAAAATCACCTTTCTAAACAAGAAATGCAATTTACCAGA
TCACAGAGAGCTCATGGAGAGGGATCTGGCAACTTAATGGGTCATGGAGATGGTAAAGGCAATTTTGTCTGTGGTAGAAA
CTATTGTGGT

ORF - retro_sscr_621 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.37 %
Parental protein coverage: 64.64 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMEVKPPPGRPQPDSGR----RRRRRGEEGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVV
.EVKPPPG.PQ.DS.......R...G.EGHDPKEP.QLRKLFIGGL.FETTDDSLREHFEKWGTLTDCVV
RetrocopyVEVKPPPGHPQLDSSHCRHCSRAGGG*EGHDPKEPKQLRKLFIGGLNFETTDDSLREHFEKWGTLTDCVV
ParentalMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKI-FVGGIKE
MRDPQTK.SRGFGFVTYS.VEEVDA.MCA.PHKVDG.VVEPKRAVSREDSVKPGAHLTVKKI.FVGGIK.
RetrocopyMRDPQTKCSRGFGFVTYSYVEEVDAVMCAGPHKVDGQVVEPKRAVSREDSVKPGAHLTVKKI<FVGGIK-
ParentalDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKY-HTINGHN-CEVKKALS
DTEEYNLRDYFEK.GKIETIEVMEDRQS.KKRGFAFVT.DDHDTV.K..VQKY.HTINGHN.CEVK..LS
RetrocopyDTEEYNLRDYFEK*GKIETIEVMEDRQSRKKRGFAFVTCDDHDTVFK-TVQKY>HTINGHN>CEVKNHLS
ParentalKQEMQSAGSQRGRGGGSGNFMGRGGNFGGGGGNFGRGGNFGG
KQEMQ...SQR..G.GSGN.MG.G.....G.GNF..G.N..G
RetrocopyKQEMQFTRSQRAHGEGSGNLMGHG----DGKGNFVCGRNYCG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 49 .38 RPM
SRP014902_testis 0 .00 RPM 138 .19 RPM
SRP018288_heart 0 .03 RPM 153 .18 RPM
SRP018288_kidney 0 .00 RPM 270 .20 RPM
SRP018288_liver 0 .00 RPM 179 .58 RPM
SRP018288_lung 0 .00 RPM 310 .16 RPM
SRP018856_adipose 0 .02 RPM 442 .64 RPM
SRP035408_brain 0 .03 RPM 370 .14 RPM
SRP035408_liver 0 .00 RPM 285 .07 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_621 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_621 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_621 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000001349712 retrocopies
Ficedula albicollis ENSFALG000000032151 retrocopy
Gallus gallus ENSGALG000000092501 retrocopy
Macropus eugenii ENSMEUG000000136226 retrocopies
Mus musculus ENSMUSG000000590056 retrocopies
Oryctolagus cuniculus ENSOCUG000000027432 retrocopies
Otolemur garnettii ENSOGAG000000281327 retrocopies
Pelodiscus sinensis ENSPSIG000000030111 retrocopy
Pteropus vampyrus ENSPVAG000000103802 retrocopies
Sus scrofa ENSSSCG000000002883 retrocopies
Sus scrofa ENSSSCG00000015988 6 retrocopies
Xenopus tropicalis ENSXETG000000018061 retrocopy
Xiphophorus maculatus ENSXMAG000000004391 retrocopy



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