RetrogeneDB ID: retro_ocun_483

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:69416627..69417128(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC2
• Ensembl ID: ENSOCUG00000005516
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 2, 34kDa [Source:HGNC Symbol;Acc:705]

Sequence

>retro_ocun_483
TTTGAGAAATACTTCCAATTCCAAGAAGAGGGAAAGAAGGAGGGAGCAGGGCAGTTACCCAGGGTAGGGATGAAGAGCCC
ATGTGTGTTGAGTCTAAAAAGGATAGGCACAGTAGTCTTGAGCACCATGTTTAAGGATGGCAATGATGTGGTCATTGGAA
AGGTGTTCATGCAGGAGTTCAAGAAGGACACAGAGCCAGTCACACAGCCCCCCAGGTCCTCATTAGCTACAGGGAGCCGC
CTCTGGAGCCGAAAGTCACAGAAGCTGCTGTGGGCGACATCAGCTATATCACCTTCATGCTGTTACCACAGCACACCAAC
TCAGTGCCCGAGATAACACCATCAACCTGATCCACACTTTCCAGGACTACCTGCACTACCACATTAAGCGCTCTGAGGCC
GGTATTCACACACGTATGTGGGTAAAAAGGCTGACTTCCTCAAGGTACTGAAGCATGCATGTCCAGATGCTGAGAAACAA
GAAATGAAAACAGTCACAGGG

Alignment

ORF - retro_ocun_483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.57 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FEKYFQFQEEGK-EGENRAVIHYRDDE-TMYVESKKDRVTVVFSTVFKDDDDVVIGKVFMQEFK-EGRRA
          FEKYFQFQEEGK.EG..RAV...R.DE....V.S.K...TVV.ST.FKD..DVVIGKVFMQEFK.EG.RA
Retrocopy FEKYFQFQEEGK<EGGSRAVTQGR-DE>SPCVLSLKRIGTVVLSTMFKDGNDVVIGKVFMQEFK<EGHRA

Parental  SHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNA-SARDNTINLIHTFRDYLHYHIKCSKA
          SHTAPQVL.S.REPPLE.K.T.AAVGD.I.YITF.L.P.HTN..SARDNTINLIHTF.DYLHYHIK.S.A
Retrocopy SHTAPQVLISYREPPLEPKVTEAAVGD-ISYITFMLLPQHTNS<SARDNTINLIHTFQDYLHYHIKRSEA

Parental  YIHTRM-RAKTSDFLKVLNRARPDAEKKEMKTITG
          .IHTRM...K..DFLKVL..A.PDAEK.EMKT.TG
Retrocopy GIHTRM<VGKKADFLKVLKHACPDAEKQEMKTVTG

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
SRP017611_brain	0.00 RPM	134.83 RPM
SRP017611_kidney	0.61 RPM	126.90 RPM
SRP017611_liver	0.00 RPM	47.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_483 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_483 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,