RetrogeneDB ID:

retro_cfam_1323

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:3:3806616..3807285(+)
Located in intron of:ENSCAFG00000007436
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_1323
ATGTCTAAGTCAGAGCCTCCCAAAGAGCCCGAGCAGCTGCGGAGCTCTTCATCGGAGGTTTGAGCTTCACAACGACCGAC
AAGAGTCTGAGGAGCCATTTTGAGCACTGGGGGCCGCTTCCGGACCGTGTGGTAAGGAGAGAGCCCAACACCGAGCGCTC
CAGAGGCTTTGGGTTCGTCACGTAGGCCACCGGGGCGGAGGCGGGCGCGGCCAGGAACCTGGGCCGCACAAGGTGGACGG
GAGAGTCTGGAACCAGAGGGCTGTCTCCCGAGAAGATTCTCAAAGACCCGGTGCCCACTTAACTGTGAAAAAGATTTTTG
TCGGTGGCATTAAAGAAGACACTGAAGAACATCATCTAAGAGATTATTTTGAACAGTATGGGAAAGTGGACGTGATTGAG
ATCATGACTGACGAGGCAGTGGCAAAAAGAGAGGTTTCGCTTTTGTGGCCTTTGCCGACCACGACTCTGTAGACAAGATT
GTCATTCAAAAATACCACACTGTGAAGGGCCACAACTGTGAAGTAAGGAAAGCCCTATGGAAGCAAGAGATGGCTAGAGC
TCCGTCCAGCCAAAGAGGCCGAAGTGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGCTGGTGTTGGTGGGAATGACAGCT
TTGGTCGTGGAGGGAACTTCAGTGGTCGA

ORF - retro_cfam_1323 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.77 %
Parental protein coverage: 60.32 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSKSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD
MSKSE.PKEPEQLR..LFIGGLSF.TTD.SLRSHFE.WG.L.D.VV.R.PNT.RSRGFGFVT.AT..E..
RetrocopyMSKSEPPKEPEQLR<ELFIGGLSFTTTDKSLRSHFEHWGPLPDRVVRREPNTERSRGFGFVT*ATGAEAG
ParentalAAMNAR-PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT
AA.N...PHKVDGRV....RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK..VIEIMT
RetrocopyAARNLG<PHKVDGRVWN-QRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKVDVIEIMT
ParentalD-RGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRG
D.RGSGKKRGFAFV.F.DHDSVDKIVIQKYHTV.GHNCEVRKAL.KQEMA.A.SSQRGRSGSGNFGGGRG
RetrocopyD<RGSGKKRGFAFVAFADHDSVDKIVIQKYHTVKGHNCEVRKALWKQEMARAPSSQRGRSGSGNFGGGRG
ParentalGGFGGNDNFGRGGNFSGR
.G.GGND.FGRGGNFSGR
RetrocopyAGVGGNDSFGRGGNFSGR

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 .07 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_1323 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1323 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1323 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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