RetrogeneDB ID: retro_cfam_513

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:25641925..25642434(-)
• Located in intron of: ENSCAFG00000002470

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC2
• Ensembl ID: ENSCAFG00000014618
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 2, 34kDa [Source:HGNC Symbol;Acc:705]

Sequence

>retro_cfam_513
ATGGTCAGTGTATCTTTGAAATTCTACAAGGAACTTTGGGCACATAGTGCTGATGAGTTATTAAAGAGGGTGTACGAGAG
TTTCTTAGTAAATCCCAAATCAGGATACAATGTCTTTTTATCATATGATCTCGAAAATCTGCCAGCATCCAAGGATTCCA
TTGTGCATCAGACTGGCATCTTGAAACTCAATTGTTTTGCCTCCGTCTTTGAGAAATACTTCCAATTTCAAGAAACCACA
AGGAAGGAGAGAACAGGGCAGTTATCCATTATAGGGATGATGAGACCATGTATGTTGAGTCTAAAAAGGACAGAGTCACA
GTAATCTTCAGCACAGTGTTTAAGGATGATGACGATGTGGTCATTGGAAAAGTGTTCATGCAGGAGTTCAAAGGAGGACA
TGGAGCCAGCCACACAGCCCCATAGGTCCTCTTTAGCTACCGGGAACCTCCTCTGGAGCTGAAAGAAATGGAGGCTATGG
TGGGTGACAACACTGGTTATATTACCTTT

Alignment

ORF - retro_cfam_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 93.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVSISLKFYKELQAHGADELLKRVYGSFLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVF
          MVS.SLKFYKEL.AH.ADELLKRVY.SFLVNP.SGYNV.L.YDLENLPASKDSIVHQ.G.LK.NCFASVF
Retrocopy MVSVSLKFYKELWAHSADELLKRVYESFLVNPKSGYNVFLSYDLENLPASKDSIVHQTGILKLNCFASVF

Parental  EKYFQFQE-EGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKVFMQEFKEGRRASHT
          EKYFQFQE...KEGENRAVIHYRDDETMYVESKKDRVTV.FSTVFKDDDDVVIGKVFMQEFK.G..ASHT
Retrocopy EKYFQFQE<NHKEGENRAVIHYRDDETMYVESKKDRVTVIFSTVFKDDDDVVIGKVFMQEFKGGHGASHT

Parental  APQVLFSHREPPLELKDTDAAVGDNIGYITF
          AP.VLFS.REPPLELK...A.VGDN.GYITF
Retrocopy AP*VLFSYREPPLELKEMEAMVGDNTGYITF

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	53.59 RPM
SRP017611_brain	0.00 RPM	63.99 RPM
SRP017611_kidney	0.00 RPM	91.66 RPM
SRP017611_liver	0.00 RPM	23.78 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_513 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_513 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003197	2 retrocopies	retro_amel_1771, retro_amel_1846,
Canis familiaris	ENSCAFG00000014618	1 retrocopy	retro_cfam_513 ,
Choloepus hoffmanni	ENSCHOG00000010564	5 retrocopies	retro_chof_1845, retro_chof_2103, retro_chof_2226, retro_chof_2227, retro_chof_473,
Dasypus novemcinctus	ENSDNOG00000006037	1 retrocopy	retro_dnov_5,
Dipodomys ordii	ENSDORG00000016107	1 retrocopy	retro_dord_624,
Felis catus	ENSFCAG00000002370	1 retrocopy	retro_fcat_732,
Loxodonta africana	ENSLAFG00000007414	1 retrocopy	retro_lafr_593,
Myotis lucifugus	ENSMLUG00000004161	1 retrocopy	retro_mluc_390,
Mustela putorius furo	ENSMPUG00000016512	1 retrocopy	retro_mputfur_1294,
Mus musculus	ENSMUSG00000006304	1 retrocopy	retro_mmus_1556,
Oryctolagus cuniculus	ENSOCUG00000005516	1 retrocopy	retro_ocun_483,
Pteropus vampyrus	ENSPVAG00000017133	1 retrocopy	retro_pvam_1216,
Sorex araneus	ENSSARG00000003326	1 retrocopy	retro_sara_283,
Tarsius syrichta	ENSTSYG00000001037	1 retrocopy	retro_tsyr_557,