RetrogeneDB ID: retro_cfam_1727

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:25225391..25225758(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2orf76
• Ensembl ID: ENSCAFG00000004896
• Aliases: None
• Description: chromosome 2 open reading frame 76 [Source:HGNC Symbol;Acc:27017]

Sequence

>retro_cfam_1727
ATGACTTCTGGAGAAGTGACCATTACAGTTTGTCTCATTCATTCATCTGAGAATCACAAATACAAACCTGTAGTAGATCA
TGGAGTTAATTTGGAGTACAATGTAAAGGAATTTAGAGTATTTCTAAAGCAAGATGCCTCTTTAAGGACCAGCCTGCACC
ACCATTCAGAAATTATAAATATGATAAACTAAAGACAACTCATCAAGCAATAAATCAAAGACAGATTAACTTGTGTTGAG
TTTGAAAAATGACAGACCCCTGTTAAAAGAAGGTAGTAATCTGAAAGCTAGAATCAACAATGAAACTGAAATTGCATTCT
TCTGTGAAGAGGATTATGAGAACTACAAAGCTAATCCCATTTCATCC

Alignment

ORF - retro_cfam_1727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.72 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASKEVTITVRLIRSFEHRNFKPIVYHGVNLDQTTKEFIVFLKQDIPLRTSL-PPPFRNYKYDKLKIVHQ
          M.S.EVTITV.LI.S.E....KP.V.HGVNL....KEF.VFLKQD..LRTSL..PPFRNYKYDKLK..HQ
Retrocopy MTSGEVTITVCLIHSSENHKYKPVVDHGVNLEYNVKEFRVFLKQDASLRTSL<APPFRNYKYDKLKTTHQ

Parental  A-HKAKTNELVLSLEDDDTLMLKEDSTLQAAGIAHETEIAFFREEDYKNYKANPISS
          A..K.KT..LVLSL..D..L.LKE.S.L.A..I..ETEIAFF.EEDY.NYKANPISS
Retrocopy A<NKSKTD*LVLSLKNDRPL-LKEGSNLKAR-INNETEIAFFCEEDYENYKANPISS

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	4.75 RPM
SRP017611_brain	0.00 RPM	4.45 RPM
SRP017611_kidney	0.00 RPM	12.94 RPM
SRP017611_liver	0.00 RPM	3.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1727 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1727 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008507	2 retrocopies	retro_amel_1062, retro_amel_1693,
Bos taurus	ENSBTAG00000010599	1 retrocopy	retro_btau_965,
Canis familiaris	ENSCAFG00000004896	2 retrocopies	retro_cfam_1119, retro_cfam_1727 ,
Equus caballus	ENSECAG00000002063	1 retrocopy	retro_ecab_384,
Myotis lucifugus	ENSMLUG00000004031	1 retrocopy	retro_mluc_1204,
Mustela putorius furo	ENSMPUG00000000943	1 retrocopy	retro_mputfur_726,
Mus musculus	ENSMUSG00000026388	1 retrocopy	retro_mmus_947,
Pteropus vampyrus	ENSPVAG00000011615	1 retrocopy	retro_pvam_337,
Sus scrofa	ENSSSCG00000015718	1 retrocopy	retro_sscr_311,