RetrogeneDB ID: retro_cfam_1395

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:90688122..90688556(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000030802
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ALYREF
• Ensembl ID: ENSCAFG00000005877
• Aliases: None
• Description: Aly/REF export factor [Source:HGNC Symbol;Acc:19071]

Sequence

>retro_cfam_1395
ATAGATTTCGGAGTGTCGGACACGGATATTCAGGAACTCTTTGCTGAATCCGGAACTCTGAAGAAGGCAGCTGTACAGCA
TGACCGCTCCGGGCGCAGTTTAGGAACAGCCGATGTGCACTTTGAACGGAAGGCAGATGCCCTGAAAGCCAGAAGCAGTA
CGACGGCGTCCCCGTGGATGGGCGCCCCGTGAACATTCAGCTCGTCTCGTCACGGACTGACACAGCGGAGACCCGCGCAG
AGCATAGCAGAGGTGGGATGACTGGAAACCGGGGCTCCGGAGGTTTCGGTGGTGGTGGCGGCGGCACCAGGAGAGGCACT
CGTGGAGGGAGCCGGGGCAGAGGTCGAGGCACTGGTGGGAGTTTGAAGCAGCAGCTTTCTGCAGAGGAGTTGGACGCCCA
GCTGGATGCTTATGACGCCAGAGTGGACACCAGC

Alignment

ORF - retro_cfam_1395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 56.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKA-MKQYNGVPLDGRPMNIQLV
          .DFGVSD.DIQELFAE.GTLKKAAV..DRSGRSLGTADVHFERKADALKA..KQY.GVP.DGRP.NIQLV
Retrocopy IDFGVSDTDIQELFAESGTLKKAAVQHDRSGRSLGTADVHFERKADALKA<QKQYDGVPVDGRPVNIQLV

Parental  TSQIDTQRRPAQSVNRGGMTRNRGSGGF-GGGGGTRRGTRGGSRGRGRGTGRSSKQQLSAEELDAQLDAY
          .S..DT....A....RGGMT.NRGSGGF.GGGGGTRRGTRGGSRGRGRGTG.S.KQQLSAEELDAQLDAY
Retrocopy SSRTDTAETRAEH-SRGGMTGNRGSGGFGGGGGGTRRGTRGGSRGRGRGTGGSLKQQLSAEELDAQLDAY

Parental  NARMDTS
          .AR.DTS
Retrocopy DARVDTS

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	47.21 RPM
SRP017611_brain	0.00 RPM	14.05 RPM
SRP017611_kidney	0.00 RPM	17.63 RPM
SRP017611_liver	0.00 RPM	9.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1395 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1395 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005877	1 retrocopy	retro_cfam_1395 ,
Gorilla gorilla	ENSGGOG00000013935	1 retrocopy	retro_ggor_2523,
Macaca mulatta	ENSMMUG00000012884	1 retrocopy	retro_mmul_1679,
Mus musculus	ENSMUSG00000025134	1 retrocopy	retro_mmus_286,
Sarcophilus harrisii	ENSSHAG00000010459	1 retrocopy	retro_shar_332,
Tupaia belangeri	ENSTBEG00000005834	7 retrocopies	retro_tbel_237, retro_tbel_2432, retro_tbel_251, retro_tbel_2690, retro_tbel_2918, retro_tbel_3933, retro_tbel_3934,