RetrogeneDB ID: retro_dord_624

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_4210:59068..59533(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arpc2
• Ensembl ID: ENSDORG00000016107
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 2 [Source:MGI Symbol;Acc:MGI:1923959]

Sequence

>retro_dord_624
TTATTAAAGAGGGTGGACAGAAGCTTCTTAGTAAACCCAGAATCAGGATACAATAGTTCTTTGCTATTTGACCTTGAAAA
TCTGCCTGCTTCCAAGGATTCCATTGTGCATCAGGCTGGCATGTTGAAGCAAAATTGTTTTGCCTCTGTCTTTGAAAAAT
GCTTCCAGTTCCAAGAAGAGGGAAAGGAAGGAGAAAACAGGGATGTTATCCATTTTAGGGATGAGACCATATATGTTGAA
TCTAAAAAGGACAGAGTCACAATAGTCTTCAGCACATTGTTTAAGGATGATGATAATGTGGTCATTGGAAAGGAGTTCAA
AGAAGGACGCAGAGCCAGCTCCCCAACCCCCCAGGTCATTTTTAGCCACAGGGAACCTCCTCTGAAGCTGAAAGACACAG
ATGCTGCTGTGGGCGACATTGGCTACATCACCTTTGTGCTGTTCCCTCACCACACCAATGCTACT

Alignment

ORF - retro_dord_624 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.09 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLKRVYGSFLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVFEKYFQFQEEGKEGENRAVI
          LLKRV..SFLVNPESGYN.SLL.DLENLPASKDSIVHQAGMLK.NCFASVFEK.FQFQEEGKEGENR.VI
Retrocopy LLKRVDRSFLVNPESGYNSSLLFDLENLPASKDSIVHQAGMLKQNCFASVFEKCFQFQEEGKEGENRDVI

Parental  HYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKVFMQEFKEGRRASHTAPQVLFSHREPPLELKDTDA
          H.R.DET.YVESKKDRVT.VFST.FKDDD.VVIGK....EFKEGRRAS...PQV.FSHREPPL.LKDTDA
Retrocopy HFR-DETIYVESKKDRVTIVFSTLFKDDDNVVIGK----EFKEGRRASSPTPQVIFSHREPPLKLKDTDA

Parental  AVGDNIGYITFVLFPRHTNAT
          AVGD.IGYITFVLFP.HTNAT
Retrocopy AVGD-IGYITFVLFPHHTNAT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_624 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,