RetrogeneDB ID: retro_ogar_1513

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873550.1:3326878..3327631(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSOGAG00000013284
• Aliases: None
• Description: COP9 signalosome subunit 2 [Source:HGNC Symbol;Acc:30747]

Sequence

>retro_ogar_1513
TTGACAAAGTTTCCAAAATTGATGACTAGATATAAACAACTATTGACCTATATTTGGAGTGCAGTCACAAGAAATTCTTC
TGAAAATTCCATTAATTCTATTCTTGATTATATCTCCACTTCTAAACAGGTGGATTTACTGCAGGAATTCTATGAAACAA
CACTGGAAGCCTTAAAAGATGCTAAGAATGAGAGACTGTGGTTTAGACAAACCCAAAGTTGGAAAATCATATTTAGAATG
AGAGGAATATGGAAAGCTCCAAAAAATGTTATCCCAGTTACATCAATCCTGCCAGACTGAAGATGGAGAATATAAGTTTA
AAAAAGGTGCACAGTTAGAAATATTTGCGTTGGAAATTCAAACGTACACAACACAGAAAAATAACAAAAAACTCAAAGCA
TTTTATGAACAGTCACTTCATACCAAGTCTGCCATCCTCATTCACTGGTCATGGGAGTTATCAGAGGATGTGGTAGTAAA
ATGCACTTGAGAGAAGGTGAGTTTGAAAAGGTACACACTGATTTTTTTGAAGCCTTTAAAAATTAGGATGACTCAGGAAG
TCCAAGATGAACCACTTGCTTAAAATATTTGGTCTTAGCAGATATGCTAGTGAAATTGGGAATTAATCCATTTGACTCAT
GGGAGGCCAAGCCATACAAAAATGATCCAGAAAGTTTAGCAATGACGAATTTAGTAAGCGCCTATCAGAATAATGACATT
ACTGAATTTGAAAAGATTGGGAAAACAAATCAC

Alignment

ORF - retro_ogar_1513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.27 %
• Parental protein coverage: 55.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNRYKQLLTYIRSAVTRNYSEKSINSILDYISTSKQNSDFLCQMDLLQEFYETTLEALKDAKNDRLWFK-
          ......L.T......T...S....NS....I...........Q.DLLQEFYETTLEALKDAKN.RLWF..
Retrocopy LTKFPKLMTRYKQLLTYIWSAVTRNSSENSINSILDYISTSKQVDLLQEFYETTLEALKDAKNERLWFR<

Parental  TNTKL-GKLYLEREEYGKLQKILRQLHQSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYE
          TN.KL.GK.YLE.EEYGKLQK.L.QLHQSCQT.DGE...KKG.QL.EI.ALEIQ.YT.QKNNKKLKA.YE
Retrocopy TNPKL<GKSYLE*EEYGKLQKMLSQLHQSCQTEDGEYKFKKGAQL-EIFALEIQTYTTQKNNKKLKAFYE

Parental  QSLHIKSAI-PHPLIMGVIRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMK
          QSLH.KSAI.PH.L.MGVIR.CG.KMHLREGEFEK.HTDFFEAFKN.D.SGSPR.TTCLKYLVLA.ML.K
Retrocopy QSLHTKSAI<PHSLVMGVIRGCGSKMHLREGEFEKVHTDFFEAFKN*DDSGSPR*TTCLKYLVLADMLVK

Parental  SGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKILKTNH
          .GINPFDS.EAKPYKNDPE.LAMTNLVSAYQNNDITEFEKI.KTNH
Retrocopy LGINPFDSWEAKPYKNDPESLAMTNLVSAYQNNDITEFEKIGKTNH

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1513 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013425	1 retrocopy	retro_btau_452,
Choloepus hoffmanni	ENSCHOG00000013375	7 retrocopies	retro_chof_1083, retro_chof_1288, retro_chof_2209, retro_chof_2371, retro_chof_2520, retro_chof_2550, retro_chof_678,
Callithrix jacchus	ENSCJAG00000001585	2 retrocopies	retro_cjac_3105, retro_cjac_3117,
Echinops telfairi	ENSETEG00000019523	2 retrocopies	retro_etel_2160, retro_etel_88,
Macaca mulatta	ENSMMUG00000009838	1 retrocopy	retro_mmul_62,
Monodelphis domestica	ENSMODG00000002466	1 retrocopy	retro_mdom_891,
Oryctolagus cuniculus	ENSOCUG00000006455	1 retrocopy	retro_ocun_1296,
Otolemur garnettii	ENSOGAG00000013284	1 retrocopy	retro_ogar_1513 ,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497,
Tursiops truncatus	ENSTTRG00000000462	1 retrocopy	retro_ttru_328,