RetrogeneDB ID: retro_cfam_616

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:6335409..6335874(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000024768
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000014018
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:E2RQS7]

Sequence

>retro_cfam_616
AAGTGTTTCAAAGGTACTGAAAATATAAGTAAAGTGTCTGAGCAGGTGAAAAATGTGAAGCTTAATGAAGATAAACCCAA
AGAAACCAAGTGTGAAGAGACTCTGGATGAGGGTCCACCAAAATATACAAAATCTGTCCTTAAAAAAGGAGATAAAACCA
ACTTTCCCAAAAAGGGAGATGTTGTTCACTGCTGGTATACAGGAACACTACAGGATGGGACTGTTTTTGATACTAATATT
CAAACCAGTTCAAAGAAGAAGAAAAATGCCAAGCCTTTAAGTTTTAAGGTTGGAATAGGCAAAGTTATCAGAGGATGGGA
CGAAGCACTCTTAACTATGAGTAAAGGAGAAAAGGCTCAACTAGAAACTGAACCAGAATGGGCTTATGGAAAGAAAGGAC
AGCCTGATGCCAAAATTCCACCAAATGCAAAACTCATTTTTGAAGTGGAATTAGTGGATATTGAT

Alignment

ORF - retro_cfam_616 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 69.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRFKGTESISKVSEQVKNVKLNEDKPKETKCEETLDEGPPKYTKSVLKKGDKTNFPKKGDVVHCWYTGTL
          K.FKGTE.ISKVSEQVKNVKLNEDKPKETKCEETLDEGPPKYTKSVLKKGDKTNFPKKGDVVHCWYTGTL
Retrocopy KCFKGTENISKVSEQVKNVKLNEDKPKETKCEETLDEGPPKYTKSVLKKGDKTNFPKKGDVVHCWYTGTL

Parental  QDGTVFDTNIQTSSKKKKNAKPLSFKVGIGKVIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKIP
          QDGTVFDTNIQTSSKKKKNAKPLSFKVGIGKVIRGWDEALLTMSKGEKA.LE.EPEWAYGKKGQPDAKIP
Retrocopy QDGTVFDTNIQTSSKKKKNAKPLSFKVGIGKVIRGWDEALLTMSKGEKAQLETEPEWAYGKKGQPDAKIP

Parental  PNAKLIFEVELVDID
          PNAKLIFEVELVDID
Retrocopy PNAKLIFEVELVDID

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	0.04 RPM	27.68 RPM
SRP017611_brain	0.16 RPM	35.09 RPM
SRP017611_kidney	0.00 RPM	31.04 RPM
SRP017611_liver	0.00 RPM	10.30 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_616 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_616 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616 , retro_cfam_798,
Choloepus hoffmanni	ENSCHOG00000000189	1 retrocopy	retro_chof_2315,
Dipodomys ordii	ENSDORG00000009462	1 retrocopy	retro_dord_106,
Equus caballus	ENSECAG00000018299	2 retrocopies	retro_ecab_352, retro_ecab_565,
Echinops telfairi	ENSETEG00000003358	8 retrocopies	retro_etel_1114, retro_etel_1484, retro_etel_1491, retro_etel_1499, retro_etel_1774, retro_etel_2130, retro_etel_2200, retro_etel_997,
Felis catus	ENSFCAG00000027304	1 retrocopy	retro_fcat_1894,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Microcebus murinus	ENSMICG00000005808	2 retrocopies	retro_mmur_1582, retro_mmur_351,
Macaca mulatta	ENSMMUG00000016512	2 retrocopies	retro_mmul_2094, retro_mmul_735,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Mus musculus	ENSMUSG00000020949	1 retrocopy	retro_mmus_1322,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Ochotona princeps	ENSOPRG00000011126	2 retrocopies	retro_opri_204, retro_opri_600,
Procavia capensis	ENSPCAG00000011316	2 retrocopies	retro_pcap_454, retro_pcap_78,
Rattus norvegicus	ENSRNOG00000004629	1 retrocopy	retro_rnor_1165,
Ictidomys tridecemlineatus	ENSSTOG00000002249	1 retrocopy	retro_itri_650,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,
Tarsius syrichta	ENSTSYG00000002125	2 retrocopies	retro_tsyr_515, retro_tsyr_820,
Tursiops truncatus	ENSTTRG00000006664	1 retrocopy	retro_ttru_1041,