RetrogeneDB ID: retro_cfam_1054

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:35189010..35189472(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000005271
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C16orf87
• Ensembl ID: ENSCAFG00000003679
• Aliases: None
• Description: chromosome 16 open reading frame 87 [Source:HGNC Symbol;Acc:33754]

Sequence

>retro_cfam_1054
ATGTCTGCGAGTCGAGCCAAGAAAGTGAAGATGGCCACCAAGTCGTGCCCCGAGTGCGACCAGCAGGTTCCTGTTGCATG
TAAATCGTGTCCCTGTGGTTACATATTTATTAGCAGAAAACTTTTAAATGCAAAACACCCAGAGAAATCACCACCTTCTA
CAGAGAACAAGCATGAGGCCAAGAGGAGGCGAACAGAGAGAGTTAGGCGAGAGAAGATAAATTCTACAGTAAATAAGGAT
TTAGAAAACAGAAAGAGGTCTCGAAGTAACAGCCATTCAGATCATATCAGACGAGGAAGAGGAAGACCTAAAACTGCATC
TGCCAAAAAACATGAGGAAGAAAGAGAGAAACAGGAAAAGGAAATTGACATCTATGCTAACCTCTCTGATGAAAAGGCTT
TCGTGTTTTCAGTCGCCTTGGCAGAAATAAATAGAAAAATTATCAATCAAAGACTTATTCTC

Alignment

ORF - retro_cfam_1054 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSASRAKKVKMATKSCPECDQQVPVACKSCPCGYIFISRKLLNAKHPEKSPPSTENKHEAKRRRTERVRR
          MSASRAKKVKMATKSCPECDQQVPVACKSCPCGYIFISRKLLNAKHPEKSPPSTENKHEAKRRRTERVRR
Retrocopy MSASRAKKVKMATKSCPECDQQVPVACKSCPCGYIFISRKLLNAKHPEKSPPSTENKHEAKRRRTERVRR

Parental  EKINSTVNKDLENRKRSRSNSHSDHIRRGRGRPKTASAKKHEEEREKQEKEIDIYANLSDEKAFVFSVAL
          EKINSTVNKDLENRKRSRSNSHSDHIRRGRGRPKTASAKKHEEEREKQEKEIDIYANLSDEKAFVFSVAL
Retrocopy EKINSTVNKDLENRKRSRSNSHSDHIRRGRGRPKTASAKKHEEEREKQEKEIDIYANLSDEKAFVFSVAL

Parental  AEINRKIINQRLIL
          AEINRKIINQRLIL
Retrocopy AEINRKIINQRLIL

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	3.95 RPM
SRP017611_brain	0.24 RPM	4.84 RPM
SRP017611_kidney	0.13 RPM	3.04 RPM
SRP017611_liver	0.00 RPM	0.80 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1054 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1054 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1054 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003679	1 retrocopy	retro_cfam_1054 ,
Cavia porcellus	ENSCPOG00000010228	2 retrocopies	retro_cpor_1197, retro_cpor_1228,
Dasypus novemcinctus	ENSDNOG00000006412	2 retrocopies	retro_dnov_1512, retro_dnov_2463,
Tupaia belangeri	ENSTBEG00000013316	2 retrocopies	retro_tbel_3011, retro_tbel_305,
Tarsius syrichta	ENSTSYG00000008921	1 retrocopy	retro_tsyr_1758,