RetrogeneDB ID:

retro_cfam_892

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:2:29585714..29586330(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA1L2
Ensembl ID:ENSCAFG00000006580
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]


Retrocopy-Parental alignment summary:






>retro_cfam_892
ATGTCTAAGTCAGAGTCTCCCAAAGACCCTCAACAGCTGCAGGAGCTCTTCATCAGGGTTTGAGCTTTGAAACAACTGTT
GAGAGTCTAAGGAGCTATTTTTGAGCAACGGGGAATGCTTACGGACTGTGTGGTAATGAGAGATCCAAACACCTACTGCT
CCAGGGGCCTTGGGTTTGTCACATATGCCACTCTGAAGGAGGAGGTGAATTCAACCATCAATGCAGGGCCAAACAAGGTA
GGTGGAAGAGATGTGGAACCAAAGAGGGCTGTCTCAAGAGAAGATTCTCAAAGACCTGGTGCCCACTTAGTTGTGAAAAA
GATTTTTGTTGGTAACATTAGAGAAGACACAGAAGAACATCATCTAAGAGATTATTTTTGAACAGTACTGGAAAATTAAA
GTGTTTGAGATCATAACTGAGCAAGGCAGTAGCTAAATGAGAGGTTTTGCTTTTGTGACATTTGATGACCAGGACTCCGG
AGACAAGATTATCATTAAAAAATCCCATACTGTGAATGGCCACAACTGTGAAGTAAGGAAAGACTTATCTAAGCAAGAGA
TGGCTAGTGCTTCATCCAGACAAAGAGTTTGAAGTGGTTCTGGAAACTTTGGTGGT

ORF - retro_cfam_892 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.88 %
Parental protein coverage: 54.69 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSKSESPKEPEQLRKLFIG-GLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATV-EE
MSKSESPK.P.QL..LFI..GLSFETT.ESLRS.F.EQ.G.LTDCVVMRDPNT..SRG.GFVTYAT..EE
RetrocopyMSKSESPKDPQQLQELFIR<GLSFETTVESLRSYF>EQRGMLTDCVVMRDPNTYCSRGLGFVTYATLKEE
ParentalVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF-EQYGKIEVIEI
V....NA.P.KV.GR.VEPKRAVSREDSQRPGAHL.VKKIFVG.I.EDTEEHHLRDYF.EQY.KI.V.EI
RetrocopyVNSTINAGPNKVGGRDVEPKRAVSREDSQRPGAHLVVKKIFVGNIREDTEEHHLRDYF>EQYWKIKVFEI
ParentalMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGG
.T..GS...RGFAFVTFDD.DS.DKI.I.K.HTVNGHNCEVRK.LSKQEMASASS.QR..SGSGNFGG
RetrocopyITEQGSS*MRGFAFVTFDDQDSGDKIIIKKSHTVNGHNCEVRKDLSKQEMASASSRQRV*SGSGNFGG

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
SRP012049_cerebellum 0 .00 RPM 309 .95 RPM
SRP017611_brain 0 .00 RPM 85 .58 RPM
SRP017611_kidney 0 .00 RPM 187 .02 RPM
SRP017611_liver 0 .00 RPM 97 .89 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_892 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_892 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_892 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000002412 retrocopies
Canis familiaris ENSCAFG00000006580 16 retrocopies
Canis familiaris ENSCAFG000000089401 retrocopy
Canis familiaris ENSCAFG0000001349712 retrocopies
Dasypus novemcinctus ENSDNOG000000092287 retrocopies
Macaca mulatta ENSMMUG000000129895 retrocopies
Mustela putorius furoENSMPUG000000046201 retrocopy
Mustela putorius furoENSMPUG000000057352 retrocopies
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
Otolemur garnettii ENSOGAG000000297073 retrocopies
Oreochromis niloticus ENSONIG000000122481 retrocopy



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