RetrogeneDB ID: retro_mmus_1556

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:20661557..20662067(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arpc2
• Ensembl ID: ENSMUSG00000006304
• Aliases: Arpc2, 2210023N03Rik, 34kDa, p34-Arc
• Description: actin related protein 2/3 complex, subunit 2 [Source:MGI Symbol;Acc:MGI:1923959]

Sequence

>retro_mmus_1556
ATGATCCTGCTGGAGGTGAACAACCGCATTATTGAGGAGAAGCTCGCACTCAAGTTCGAGAACGTGTCCGCTGGAAACAA
ACCAGAAGCTGTAGAAGTAACATTTGCAGATTTTGATGGTGTCCTTTATCATATTTCAAGTCCTAATGGAGACAAAACAA
AAGTGATGGTCAGTATTTCCTTGAAATTCTACAAGGAACTTCAGGCACATGGAGCTGATGAGTTATTAAAGAGAGTATAT
GGGAGTTTCTTGGTAAGTCCAGAACCAGGATATAATGTTTCTTTGCTATATGACTTGGAAAATCTACCTGCATCCAAGAA
TTCTATTGTGCATCAGGCTGGCATGTTGAAGCGAAATTGTTTTGCCTCTATGTTTGAGAAATACTTCCAATTCCAAGAAG
AGGGCAAAGAAGGAGAGAACATAGCAGTTATCCATTATAGGGATGATGAGACCATGTATGTGGAATCTCAGAAAGACAGA
GTCACAGTAGTCTTCAGCACAGTTTTTAAA

Alignment

ORF - retro_mmus_1556 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.71 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSISLKFYKELQAH
          MILLEVNNRIIEE.LALKFEN..AGNKPEAVEVTFADFDGVLYHIS.PNGDKTKVMVSISLKFYKELQAH
Retrocopy MILLEVNNRIIEEKLALKFENVSAGNKPEAVEVTFADFDGVLYHISSPNGDKTKVMVSISLKFYKELQAH

Parental  GADELLKRVYGSFLVNPEPGYNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVFEKYFQFQEEGKEGEN
          GADELLKRVYGSFLV.PEPGYNVSLLYDLENLPASK.SIVHQAGMLKRNCFAS.FEKYFQFQEEGKEGEN
Retrocopy GADELLKRVYGSFLVSPEPGYNVSLLYDLENLPASKNSIVHQAGMLKRNCFASMFEKYFQFQEEGKEGEN

Parental  RAVIHYRDDETMYVESKKDRVTVVFSTVFK
          .AVIHYRDDETMYVES.KDRVTVVFSTVFK
Retrocopy IAVIHYRDDETMYVESQKDRVTVVFSTVFK

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
SRP007412_brain	0.05 RPM	125.32 RPM
SRP007412_cerebellum	0.04 RPM	70.21 RPM
SRP007412_heart	0.09 RPM	87.72 RPM
SRP007412_kidney	0.04 RPM	122.72 RPM
SRP007412_liver	0.05 RPM	91.40 RPM
SRP007412_testis	0.05 RPM	103.64 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1556 was not detected

EST

No EST(s) were mapped for retro_mmus_1556 retrocopy.

TSS

No TSS is located nearby retro_mmus_1556 retrocopy 5' end.

Lab

retro_mmus_1556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1556 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,