RetrogeneDB ID: retro_cfam_852

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:37372955..37373248(+)
• Located in intron of: ENSCAFG00000005012

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBY1
• Ensembl ID: ENSCAFG00000001384
• Aliases: None
• Description: chibby homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:1307]

Sequence

>retro_cfam_852
ATGCCTCTCTTTGGGAATACGTTCAGTCCTTAGAAAACGTTCGCTTCTCTCTCCAAACTGCATAATCTGGATTGGTCAAC
CCAGGAGGTGAAGCTGGGCCTGGACTATGGAACCCCCACCATGAACGTGGTGGGACAAAGCCTGAAGTTTGAAAATGGCC
AGTGGATAGCAGAGTCGGGGATTAGTGGAGGTGTGGCCCGGAGGGAGCTCAGCAGCTCCGCAGGCGGAACCAGCAAGTGG
AGAAAGACGACAATCTCTTGAGGCTAAAGGTGGACACCCTGCTGGACATGCTG

Alignment

ORF - retro_cfam_852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.73 %
• Parental protein coverage: 80.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPLFGNTFSPKKTPPRKSASLSNLHNLDRSTREVELGLDYGTPTMNLAGQSLKFENGQWIAETGISEDVD
          MPLFGNTFS....P....ASLS.LHNLD.ST.EV.LGLDYGTPTMN..GQSLKFENGQWIAE.GIS..V.
Retrocopy MPLFGNTFS----P*KTFASLSKLHNLDWSTQEVKLGLDYGTPTMNVVGQSLKFENGQWIAESGISGGVA

Parental  RRE-AQRLRRRNQQLEEENNLLRLKVDILLDML
          RRE.AQ.LRRRNQQ.E...NLLRLKVD.LLDML
Retrocopy RRE<AQQLRRRNQQVEKDDNLLRLKVDTLLDML

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	6.17 RPM
SRP017611_brain	0.00 RPM	4.84 RPM
SRP017611_kidney	0.00 RPM	10.43 RPM
SRP017611_liver	0.00 RPM	2.39 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_852 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_852 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001384	2 retrocopies	retro_cfam_1396, retro_cfam_852 ,
Dasypus novemcinctus	ENSDNOG00000010982	1 retrocopy	retro_dnov_875,
Homo sapiens	ENSG00000100211	1 retrocopy	retro_hsap_2344,
Gorilla gorilla	ENSGGOG00000013226	1 retrocopy	retro_ggor_1781,
Myotis lucifugus	ENSMLUG00000003757	2 retrocopies	retro_mluc_1128, retro_mluc_2608,
Mustela putorius furo	ENSMPUG00000013150	1 retrocopy	retro_mputfur_1186,
Nomascus leucogenys	ENSNLEG00000015153	1 retrocopy	retro_nleu_349,
Otolemur garnettii	ENSOGAG00000028533	1 retrocopy	retro_ogar_1072,
Pan troglodytes	ENSPTRG00000014373	1 retrocopy	retro_ptro_1716,
Vicugna pacos	ENSVPAG00000001484	1 retrocopy	retro_vpac_57,