RetrogeneDB ID: retro_cfam_740

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:43966454..43967008(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000002903
• Aliases: None
• Description: None

Sequence

>retro_cfam_740
CTTTGGGTCCTGTACAAAGACAAGTCCAAAGCAGTGCTGCTTAAGACAGTGGATGACATGTCCTCCTTCAGCTTCTTCCA
GAGGTCCAGTGTTTAGGAGTCCATGACCTTCACAAGTCAACCGATTGTGGAGCACTCAGAGAAAGGCCACAGAGCTTCTG
TCAAAGCACATCTGTGCCACATCTTTGTACAACATGACAGTCTTGCAGGAATGGTCATAATGGACAGTGAATATCCATTC
TGGGTGGCCTTTGCCTTGCCGGAGAAGGTACTGGATGAATTCTCCAAGCAGGTTGACAAGATAGAGTGGCCAATCAGATC
CCCTGTACCATCCACTGTGTCTCCCTAGATGGCCACCTCAGGAGATACCAGAACCTCAGAGAAGCTGACACCAGGCCTAA
AGTGCAGACTGAGTTGGATGCGATCAAAATCATTCTGCACAACACCATGGAGCCTCTGTTGGAGTTGGGGGAGAAGCTAG
ATGGCCTGGTATCCAAATCCAAAGTGCTGGGAACACAGTCTAAGGCCCCAAACAGAACTGGTGCAGTGCAATCA

Alignment

ORF - retro_cfam_740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.89 %
• Parental protein coverage: 94.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSVLYKGEPKGFIAKTSLFGALFPMVERESVQEFMTFTSQLIVERSAKGSRASVKEQEYLCHVYVRNDSL
          L.VLYK...K....KT......F....R.SV.E.MTFTSQ.IVE.S.KG.RASVK....LCH..V..DSL
Retrocopy LWVLYKDKSKAVLLKTVDDMSSFSFFQRSSV*ESMTFTSQPIVEHSEKGHRASVKA--HLCHIFVQHDSL

Parental  AGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIEWPIGSPA-SIHYTALDGHLSRYQNPREADPMTKVQA
          AG.VI.DSEYP..VAF.L.EKVLDEFSKQVD.IEWPI.SP...IH...LDGHL.RYQN.READ...KVQ.
Retrocopy AGMVIMDSEYPFWVAFALPEKVLDEFSKQVDKIEWPIRSPV<TIHCVSLDGHLRRYQNLREADTRPKVQT

Parental  ELDETKIILHNTMESLLERGEKLDDLVSKSEVLGTQSKAFYKTARKQN
          ELD..KIILHNTME.LLE.GEKLD.LVSKS.VLGTQSKA...T...Q.
Retrocopy ELDAIKIILHNTMEPLLELGEKLDGLVSKSKVLGTQSKAPNRTGAVQS

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	15.75 RPM
SRP017611_brain	0.00 RPM	14.21 RPM
SRP017611_kidney	0.07 RPM	45.24 RPM
SRP017611_liver	0.07 RPM	11.17 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_740 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017618	1 retrocopy	retro_amel_967,
Bos taurus	ENSBTAG00000000274	1 retrocopy	retro_btau_601,
Canis familiaris	ENSCAFG00000002903	1 retrocopy	retro_cfam_740 ,
Choloepus hoffmanni	ENSCHOG00000011207	1 retrocopy	retro_chof_657,
Callithrix jacchus	ENSCJAG00000008053	2 retrocopies	retro_cjac_2394, retro_cjac_2492,
Dasypus novemcinctus	ENSDNOG00000015173	1 retrocopy	retro_dnov_1364,
Dipodomys ordii	ENSDORG00000016393	1 retrocopy	retro_dord_621,
Erinaceus europaeus	ENSEEUG00000001247	1 retrocopy	retro_eeur_267,
Felis catus	ENSFCAG00000014362	1 retrocopy	retro_fcat_1327,
Homo sapiens	ENSG00000106636	1 retrocopy	retro_hsap_3687,
Gorilla gorilla	ENSGGOG00000027036	1 retrocopy	retro_ggor_2493,
Macropus eugenii	ENSMEUG00000014769	1 retrocopy	retro_meug_2068,
Mustela putorius furo	ENSMPUG00000018200	2 retrocopies	retro_mputfur_141, retro_mputfur_165,
Mus musculus	ENSMUSG00000002741	1 retrocopy	retro_mmus_825,
Nomascus leucogenys	ENSNLEG00000003689	1 retrocopy	retro_nleu_2275,
Oryctolagus cuniculus	ENSOCUG00000002981	1 retrocopy	retro_ocun_15,
Pongo abelii	ENSPPYG00000017595	1 retrocopy	retro_pabe_3022,
Pan troglodytes	ENSPTRG00000019141	1 retrocopy	retro_ptro_2500,
Sus scrofa	ENSSSCG00000016750	1 retrocopy	retro_sscr_1063,
Tursiops truncatus	ENSTTRG00000006052	2 retrocopies	retro_ttru_1320, retro_ttru_417,