RetrogeneDB ID: retro_cfam_477

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:2474417..2475442(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATP6V0D2
• Ensembl ID: ENSCAFG00000008749
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2 [Source:HGNC Symbol;Acc:18266]

Sequence

>retro_cfam_477
CTGAGCTTTAACATGGACCTTAGCCACCTGGAAGGCCTGCTGTGAGGGGACAAAGCCAGACTCTTGACCCAGCAGGAATA
CATCAACCTGGTCCAGTGTAGCACCCTGGAAGATGTGAAAATTCATTTCCAGACCACTGATCATGGCAACTTCTTGGCTT
ATCCTCTTATGGCTTCCAAAATTGACACCAAGATGGAGAAAAAGCTATGCAGAGAATTTGGATATTTCTGGAATCATCCC
CCAGAACCCTGAGCACATTTTTTTGCATACATGATGTGCAGTTACATGACAATGTGATTCTACTGATGAACGGTGCGTTG
CCAAAAAAAAAAAAATCTGTGCAAGAAATTCTGGTGAAGTGCCACCTATTAGGCTATTTCACAGAAATGGAAACAGTCAA
CATTATGGAGACACTTTCCTATCCCTTTAATGCTGTTCTGGTTGAAATACCGTTAGCTACATTCTTTCTGGACTATATGT
CTGAAAATACTGTAGATAAACTGAATATTGAATTACTGCATAATACGCTGTACAAATCTTACCTTGAAGCATTCTATAAA
TTCTGTAAGGATCATGGTGATGTCACAGCAGAAATTATGCATCCCATTCTTGAGTTTGAGGGTACCAGAGGTGCTTTTAT
CATGACGTTTAACCCTTTGTAACCGAACTGAGTAAAGACGACCGAGAGACCCTCTACCTGACCTGTGGCAAGCTCTGTCC
TGAGCAACTATGCCTTCTGCTCAAGCAGAAGACTTTGACCAGATGAGGTGAGTAGAGGACCATTACAGACTTTACGGGCC
TTTGTTTGAGACTGTGGTCATGGCACTGGAGGAAAGACATTGGAGGATGTGTTTTATGACTATGAGGTACAAATGAAAGT
GCTGGCATTCAACATGCAATTCCACTATGGCGTGATTAACATATACACAAAGCTGAAGGAACAAGAAATGAAAAATATTG
TGTGGATAGCAGAATGCTTTTCACAAAGACATTGAAGTAATATGAACAGTTACATTCCAATTTTA

Alignment

ORF - retro_cfam_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.5 %
• Parental protein coverage: 98.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LYFNVDHGYLEGLVRGCKASLLTQQDYINLVQCETLEDVKIHLQTTDYGNFLANQTNPLTVSKIDTEMRK
          L.FN.D...LEGL..G.KA.LLTQQ.YINLVQC.TLEDVKIH.QTTD.GNFLA....PL..SKIDT.M.K
Retrocopy LSFNMDLSHLEGLL*GDKARLLTQQEYINLVQCSTLEDVKIHFQTTDHGNFLAY---PLMASKIDTKMEK

Parental  KLCREFEYFRNHSLEP-LSTFFTYMTCSYMIDNVILLMNGALQKK--SVKEILVKCHPLGRFTEMEAVNI
          KLCREF.YF.NH..EP.LSTFF.........DNVILLMNGAL.....SV.EILVKCH.LG.FTEME.VNI
Retrocopy KLCREFGYFWNHPPEP<LSTFFCIHDVQ-LHDNVILLMNGALXXXXXSVQEILVKCHLLGYFTEMETVNI

Parental  AETPSDLFNAVLVETPLAPFFQDCMSENTLDELNIELLRNKLYKSYLEAFYKFCKNHGDVTAEIMCPILE
          .ET.S..FNAVLVE.PLA.FF.D.MSENT.D.LNIELL.N.LYKSYLEAFYKFCK.HGDVTAEIM.PILE
Retrocopy METLSYPFNAVLVEIPLATFFLDYMSENTVDKLNIELLHNTLYKSYLEAFYKFCKDHGDVTAEIMHPILE

Parental  FEADRRAFIITLN-SFGTELSKDDRETLYPTCGKLYPEGLRLL-AQAEDFDQMRRVADHYGVYKPLFEAV
          FE..R.AFI.T.N..F.TELSKDDRETLY.TCGKL.PE.L.LL.AQAEDFDQMR.V.DHY..Y.PLFE.V
Retrocopy FEGTRGAFIMTFN<PFVTELSKDDRETLYLTCGKLCPEQLCLL<AQAEDFDQMR*VEDHYRLYGPLFETV

Parental  -GDGNGGKTLEDVFYEREVQMNVLAFNRQFHYGVFYAYTKLKEQEMRNIVWIAECISQRHRTKINSYIPI
          .G.G.GGKTLEDVFY..EVQM.VLAFN.QFHYGV...YTKLKEQEM.NIVWIAEC.SQRH....NSYIPI
Retrocopy <GHGTGGKTLEDVFYDYEVQMKVLAFNMQFHYGVINIYTKLKEQEMKNIVWIAECFSQRH*SNMNSYIPI

Parental  L
          L
Retrocopy L

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	0.21 RPM
SRP017611_brain	0.08 RPM	0.00 RPM
SRP017611_kidney	0.07 RPM	32.56 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_477 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_477 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_477 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008749	1 retrocopy	retro_cfam_477 ,
Callithrix jacchus	ENSCJAG00000000343	1 retrocopy	retro_cjac_515,