RetrogeneDB ID: retro_cfam_507

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:6933996..6934217(-)
• Located in intron of: ENSCAFG00000001489

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSA
• Ensembl ID: ENSCAFG00000012054
• Aliases: None
• Description: endosulfine alpha [Source:HGNC Symbol;Acc:3360]

Sequence

>retro_cfam_507
ATGTCCCAGAAACAAGAAGAGGAGAATCCTGCAGAGAAGACCGGTGTGAGGAAGCAGGGCACATGGGAAAAGAAGGCATT
CTCCCTGAGATTGCCAAGGAGGCAAAACTAAAGGCCAAATATCCAAGCCTAAGACAAAAGCCTGGAGGCTCTGACTTCCT
CATGAACAGACTCCAGAAAGGGCAAAAATACTCTGAAGCAAAACACTACAACATGCCCAAA

Alignment

ORF - retro_cfam_507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.67 %
• Parental protein coverage: 61.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQKQEEENPAEETGEEKQDTQEK-EGILPERAEEAKLKAKYPSLGQKPGGSDFLMKRLQKGQKYFDSGD
          MSQKQEEENPAE.TG..KQ.T.EK.EGILPE.A.EAKLKAKYPSL.QKPGGSDFLM.RLQKGQKY.....
Retrocopy MSQKQEEENPAEKTGVRKQGTWEK<EGILPEIAKEAKLKAKYPSLRQKPGGSDFLMNRLQKGQKYSEAKH

Parental  YNMAK
          YNM.K
Retrocopy YNMPK

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	66.44 RPM
SRP017611_brain	0.00 RPM	103.13 RPM
SRP017611_kidney	0.00 RPM	53.03 RPM
SRP017611_liver	0.07 RPM	12.69 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_507 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_507 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001375	1 retrocopy	retro_amel_1339,
Canis familiaris	ENSCAFG00000012054	1 retrocopy	retro_cfam_507 ,
Canis familiaris	ENSCAFG00000032515	2 retrocopies	retro_cfam_1375, retro_cfam_1402,
Loxodonta africana	ENSLAFG00000011261	1 retrocopy	retro_lafr_151,
Mustela putorius furo	ENSMPUG00000004647	1 retrocopy	retro_mputfur_299,
Sorex araneus	ENSSARG00000002625	1 retrocopy	retro_sara_621,