RetrogeneDB ID: retro_cfam_1608

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 37:14559043..14559323(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC2
• Ensembl ID: ENSCAFG00000011754
• Aliases: None
• Description: Trafficking protein particle complex subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:E2QV03]

Sequence

>retro_cfam_1608
AGGAGCTATATATTGAAGACAACGTCTGGAAGCTTCTATTGTGTAGTTGTTGTCCATCATGATAATCCAGTTTCTGAAAG
GGAGTTTTTGAAAGCAGAGTCCGAAGCTGGTCATCGTCGTCTGAACCAGTTCATAGCTCTTGACCTTGTAGATGAGAATC
TGTGGCTTGTCCGATGACATGTACTTGAAAACCATGGACAAGGTCAATGAGTGGCTTGTTTCAGCCTTGGTTACTGCAGG
TCATGTGGGATTTATTAGGCTCCATGACATAAGGGAAGAA

Alignment

ORF - retro_cfam_1608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.0 %
• Parental protein coverage: 52.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSYILKTMSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWL-SNNMYLK
          RSYILKT.SGSFY.V.V.HHDNPV.E.EFL...KAES...HR.LNQFI...ALDLVDEN.WL.S..MYLK
Retrocopy RSYILKTTSGSFYCVVVVHHDNPVSEREFL---KAESEAGHRRLNQFI---ALDLVDENLWL>SDDMYLK

Parental  TVDKFNEWFVSAFVTAGHMRFIMLHDIRQE
          T.DK.NEW.VSA.VTAGH..FI.LHDIR.E
Retrocopy TMDKVNEWLVSALVTAGHVGFIRLHDIREE

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	13.10 RPM
SRP017611_brain	0.08 RPM	16.20 RPM
SRP017611_kidney	0.00 RPM	13.87 RPM
SRP017611_liver	0.00 RPM	4.35 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1608 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1608 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001719	1 retrocopy	retro_acar_53,
Canis familiaris	ENSCAFG00000011754	2 retrocopies	retro_cfam_1608 , retro_cfam_368,
Homo sapiens	ENSG00000196459	1 retrocopy	retro_hsap_73,
Microcebus murinus	ENSMICG00000004690	1 retrocopy	retro_mmur_1022,
Macaca mulatta	ENSMMUG00000022619	1 retrocopy	retro_mmul_326,
Monodelphis domestica	ENSMODG00000017312	2 retrocopies	retro_mdom_1737, retro_mdom_1901,
Mus musculus	ENSMUSG00000079317	2 retrocopies	retro_mmus_198, retro_mmus_2522,
Otolemur garnettii	ENSOGAG00000002870	2 retrocopies	retro_ogar_369, retro_ogar_60,
Pan troglodytes	ENSPTRG00000021674	1 retrocopy	retro_ptro_72,
Sorex araneus	ENSSARG00000006353	1 retrocopy	retro_sara_244,
Ictidomys tridecemlineatus	ENSSTOG00000025097	1 retrocopy	retro_itri_1014,