RetrogeneDB ID: retro_cfam_1885

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:67014511..67014995(-)
• Located in intron of: ENSCAFG00000018282

Retrocopy information

• Ensembl ID: ENSCAFG00000018296
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHB2
• Ensembl ID: ENSCAFG00000014439
• Aliases: None
• Description: prohibitin 2 [Source:HGNC Symbol;Acc:30306]

Sequence

>retro_cfam_1885
CACGAGGTGCTGAAAAGCGTGGCGGCCAAGTTCAGTGCCTCGGCCCTGATCACCCGGAGGGCCCAGGTATCCTTGTGGAC
CGGCGGGAGCTGACGGAGACGCCCAGAGACTTCAGCCTCAGCCTGGAGGACGTGGCCATCACAGAGCTGGGCTTTAGCCG
AGAATACACAGCTGCTGTGGAAGCCAAACAAGTGGCCCAGCAGGAGGCCCAGCGAGCCCAGTTTTTGGTAGCAAAAGCAA
AGCAGGAGCGACGGCAGAAGACTGTGCAGGCCGAGGGTGAGGCCGAGGCCGCCAGAACGCTTGGAGAAGCCTGAGCAAGA
ACCCTGGCTGCCTCAAACTGTGCAAGATCCGGGCAGCCCAGAACGCCTCTAAGACGATCGCTACATCACAGAACCGTATT
TATCTCACCGCTGACAACCTCGTCTTGAACCTACAGGATGAAAGTTTTACCCGGGGCCGTGACAGCCTCATCAAGAGTAA
GAAG

Alignment

ORF - retro_cfam_1885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.76 %
• Parental protein coverage: 54.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NEVLKSVVAKFNASQLITQRAQVSL-LIRRELTERAKDFSLILDDVAITELSFSREYTAAVEAKQVAQQE
          .EVLKSV.AKF.AS.LIT.RAQVSL...RRELTE...DFSL.L.DVAITEL.FSREYTAAVEAKQVAQQE
Retrocopy HEVLKSVAAKFSASALITRRAQVSL<VDRRELTETPRDFSLSLEDVAITELGFSREYTAAVEAKQVAQQE

Parental  AQRAQFLVEKAKQEQRQKIVQAEGEAEAARMLGEA-LSKNPGYIKLRKIRAAQNISKTIATSQNRIYLTA
          AQRAQFLV.KAKQE.RQK.VQAEGEAEAAR.LGEA.LSKNPG..KL.KIRAAQN.SKTIATSQNRIYLTA
Retrocopy AQRAQFLVAKAKQERRQKTVQAEGEAEAARTLGEA<LSKNPGCLKLCKIRAAQNASKTIATSQNRIYLTA

Parental  DNLVLNLQDESFTRHSDSLIKSKK
          DNLVLNLQDESFTR..DSLIKSKK
Retrocopy DNLVLNLQDESFTRGRDSLIKSKK

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	0.55 RPM	87.65 RPM
SRP017611_brain	0.48 RPM	57.56 RPM
SRP017611_kidney	1.39 RPM	200.22 RPM
SRP017611_liver	2.18 RPM	209.64 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1885 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1885 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1885 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885 ,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419, retro_pabe_557, retro_pabe_559,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373,