RetrogeneDB ID: retro_cfam_1020

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:33290476..33291007(+)
• Located in intron of: ENSCAFG00000007500

Retrocopy information

• Ensembl ID: ENSCAFG00000007529
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008038
• Aliases: None
• Description: None

Sequence

>retro_cfam_1020
ATGTCGGAAGGGGAAGCCAGGCAGAGCAAAGGCTCCCCGCAGGCAGGCGCGGTGACTGTCAGTGACATCCAGGAGCTCAT
ACAGTGCAAGGAGGAGATGGAGGCACAGATCAAAGCCAATTATGACGTACTGGAGAGTCAAAAGGGCGTAGGGATGAACG
AGCTGCTGGTAGACTGTGAGGGCTACCCCGGTCAGACGTGGACCTGTACCAAGTCCGAACCGCCAGGCACAACATCATCT
GCTTGCAGAATGATCACAAGGCAGTCATGAAGCAGGTGGAGGCCCTATACCAGCTGCATGCTCGAGACAAGGAGAAGCTG
GCCTGGGACATGGCTGAGGCCCATGAAGAGGCCATGAGCCACAACTTGGGCCAGTGAGGGCCTCAGCCCCCTTCAGGCCT
TCGCCAAAGTGAACAGCATCAGTCTTGGCTCCCCTGCCAGTAATGCGGGTCTGCAAGTGGATGATGAGATTGTGGAGTTT
GGCTCTGTGAACACCCAAAACTTCCAGTCTCTGCATAACATCAGCACAGTG

Alignment

ORF - retro_cfam_1020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 80.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEGEARQGEGSPQAGAVTVSDIQELIRRKEEIEAQIKANYDVLESQKGVGMNEPLVDCEGY-PRSDVDL
          MSEGEARQ..GSPQAGAVTVSDIQELI..KEE.EAQIKANYDVLESQKGVGMNE.LVDCEGY.PRSDVDL
Retrocopy MSEGEARQSKGSPQAGAVTVSDIQELIQCKEEMEAQIKANYDVLESQKGVGMNELLVDCEGY<PRSDVDL

Parental  YQVRTARHNIVCLQNDHKAVMKQVEEALHQLHARDKEKQARDMAEAHEEAMSRNLGQSEDRRPP-QAFAK
          YQVRTARHNI.CLQNDHKAVMKQV.EAL.QLHARDKEK.A.DMAEAHEEAMS.NLGQ.....PP.QAFAK
Retrocopy YQVRTARHNIICLQNDHKAVMKQV-EALYQLHARDKEKLAWDMAEAHEEAMSHNLGQ-*GPQPP>QAFAK

Parental  VNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSLHNISNV
          VNSIS.GSPAS.AGLQVDDEIVEFGSVNTQNFQSLHNIS.V
Retrocopy VNSISLGSPASNAGLQVDDEIVEFGSVNTQNFQSLHNISTV

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	36.12 RPM
SRP017611_brain	0.00 RPM	34.62 RPM
SRP017611_kidney	0.00 RPM	33.22 RPM
SRP017611_liver	0.00 RPM	16.82 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1020 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1020 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1020 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008038	1 retrocopy	retro_cfam_1020 ,
Loxodonta africana	ENSLAFG00000008585	1 retrocopy	retro_lafr_144,
Myotis lucifugus	ENSMLUG00000013501	1 retrocopy	retro_mluc_617,
Ochotona princeps	ENSOPRG00000016588	1 retrocopy	retro_opri_839,
Tursiops truncatus	ENSTTRG00000003021	1 retrocopy	retro_ttru_499,