RetrogeneDB ID: retro_cfam_420

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:32870795..32871267(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000001476
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000013185
• Aliases: None
• Description: None

Sequence

>retro_cfam_420
CCGTGGCTGGGAGGTGGGCTGAGGCAGCTCGGGTAGGGACTCAGGGCGCAGTAGGGACACGGGGCGCGGGACAGAGCCTC
CCATCGGCTCCCCTTAGGTGCCGAGATGCTCAAGGGAGCTGGGGCAACAAACAAGGGCAAGAGCCAGGAGCTAAAGAGGA
CACCTCCTGGCTTAGGTCCTGTGGTGGTGGACCCCAGAGGTGGTGTCACCATAGCCATCCACGCCAAACCCGGGTCCAAA
CAAAACATTGTGACAGACATGAGAGCGGAAGCTGTGAGCACGGCCATCTCAGCCCCCACTTCGGAAGGAGACGCTCATGC
CAAGCCCTTTTGGTACCTGTCCAAGGTCCTGGAGCTAGGAAGAGTAAGTGGTTTTGGATGAGGGTGGTGAATCTCGTAAA
AAAGTGGTGAAGCTATTAGCATCCACAACCACTGAAGAGATCTTGGAGAAATTAAAGCAACAGGTCTAGAAA

Alignment

ORF - retro_cfam_420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.81 %
• Parental protein coverage: 56.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PGSPAGMLRLGRGLRRLLSARGAR--ASAGLPLGAEMPKKAGATNKGKSQEPERPPPSLGPVTVDPRGSV
          P....G...LG.GL.R.....GAR..AS..LPLGAEM.K.AGATNKGKSQE..R.PP.LGPV.VDPRG.V
Retrocopy PWLGGGLRQLG*GL-RAQ*GHGARDRASHRLPLGAEMLKGAGATNKGKSQELKRTPPGLGPVVVDPRGGV

Parental  TIAIRAKPGSKQNAVTDVTAEAVSVAIAAPPSEGEANAELCRYLSKVLEL-RKSD-VVLDKGGKSREKVV
          TIAI.AKPGSKQN.VTD..AEAVS.AI.AP.SEG.A.A....YLSKVLEL.RKS..VVLD.GG.SR.KVV
Retrocopy TIAIHAKPGSKQNIVTDMRAEAVSTAISAPTSEGDAHAKPFWYLSKVLEL<RKSK<VVLDEGGESRKKVV

Parental  KLLASTTAEEILEKLKQQVEK
          KLLASTT.EEILEKLKQQV.K
Retrocopy KLLASTTTEEILEKLKQQV*K

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	16.88 RPM
SRP017611_brain	0.00 RPM	13.89 RPM
SRP017611_kidney	0.00 RPM	18.03 RPM
SRP017611_liver	0.00 RPM	5.87 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_420 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_420 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_420 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016522	2 retrocopies	retro_btau_1724, retro_btau_485,
Canis familiaris	ENSCAFG00000013185	2 retrocopies	retro_cfam_39, retro_cfam_420 ,
Callithrix jacchus	ENSCJAG00000015877	2 retrocopies	retro_cjac_1108, retro_cjac_4086,
Equus caballus	ENSECAG00000022459	1 retrocopy	retro_ecab_374,
Homo sapiens	ENSG00000169609	1 retrocopy	retro_hsap_1881,
Gorilla gorilla	ENSGGOG00000023062	1 retrocopy	retro_ggor_1378,
Microcebus murinus	ENSMICG00000009564	2 retrocopies	retro_mmur_1387, retro_mmur_1601,
Myotis lucifugus	ENSMLUG00000007515	1 retrocopy	retro_mluc_2487,
Macaca mulatta	ENSMMUG00000015890	1 retrocopy	retro_mmul_664,
Monodelphis domestica	ENSMODG00000019374	1 retrocopy	retro_mdom_145,
Nomascus leucogenys	ENSNLEG00000010930	1 retrocopy	retro_nleu_1803,
Oryctolagus cuniculus	ENSOCUG00000005072	1 retrocopy	retro_ocun_211,
Procavia capensis	ENSPCAG00000016446	1 retrocopy	retro_pcap_51,
Pongo abelii	ENSPPYG00000006737	1 retrocopy	retro_pabe_1561,
Rattus norvegicus	ENSRNOG00000019514	2 retrocopies	retro_rnor_1547, retro_rnor_2334,
Sorex araneus	ENSSARG00000006314	1 retrocopy	retro_sara_147,
Sarcophilus harrisii	ENSSHAG00000017947	2 retrocopies	retro_shar_233, retro_shar_442,
Sus scrofa	ENSSSCG00000030131	1 retrocopy	retro_sscr_221,
Tupaia belangeri	ENSTBEG00000014387	6 retrocopies	retro_tbel_1151, retro_tbel_2000, retro_tbel_3071, retro_tbel_3546, retro_tbel_4182, retro_tbel_4371,