RetrogeneDB ID: retro_chof_1288

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_251213:38..1071(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSCHOG00000013375
• Aliases: None
• Description: COP9 signalosome subunit 2 [Source:HGNC Symbol;Acc:30747]

Sequence

>retro_chof_1288
TATTTGGAGTGCAGTTACACAAGAAATTATTCTGAAAAATCCATTAATTCTATTCTTGATTATATCTCCACTTCTAAACA
CTTGGATTTACTGCAGGAATTCTATGAAACAACACTGGAAGCTTTGAAAGATGCTAAGACTGATAGACTATGGCTTAAGA
CAAACACAAAGCTTGGAAAATTATATTTAGAATGTGAGGAATATGGAAAGCTTCAAAAAATTTTACTTCAATTACATCAA
TCCTGCAAGACTGATGAAGAAGATGACCTGAAAAAAGGTACACAGTAATTAAAAATAGAATTCCACCACATTGGAGCTGT
ACACAGCACAGAAGACTAACAAAAAGCTTAAAGCACTCTATGAACAGTCACTTCACATCAAGTCTGCCATCCCTCATCCA
TTGATCATGGGAGTCATCAGAGAATGTGGTGATAAAATGCACTTTAGAGAAGGTGAATTTGAAAAGGCACACACTGATTT
TTTTTGAAGTCTTCAAGAATTATGATGAATGGGGGAGTCCCAGATGAATCACTTGCTTAAAATATTTGGTCTTAGCAAAT
ATGCTAATGAAATCGGGAATAACTCCATCTGACTCACAGGCCAGGCTGTACAGAAATGATCCAGAAATTCTAGCAATGAT
GAATTTAGTAAGTGCCTATCAGAATAATGACATCACTGAATTTGAAAAGATTCTGAAAAAAATCACAGCAACATCATGGA
TGATCTTTTCATAAGGGAACATATTGAAGAGGTTTTGCAAAACACCAGAACACAAGTGGTCATAAAATTAATTAAGCCTT
ACACAAGAATACATATTCCTTTTATTTCTAAGGAGTTAAACATAGATGTAGCTGATGTGGAGAGCTTGCTGGTAGAGTGC
ATATTGGATAACACTGTTCATGGCTGAATTGATCAAGTCAACCAACTCCTTGAACTGGATCATCTGAAGAGGGGTGGTGC
ATGATATACTGCTCTAGATAAATGGACCACCCAGTTAAATTCTCTCAACCAGGCTGTAGTCAGTAAACTTGCT

Alignment

ORF - retro_chof_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.5 %
• Parental protein coverage: 78.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YIRSAVTRNYFEKSINCILDYISTNSDFLCQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLE-R
          Y.....TRNY.EKSIN.ILDYIST........DLLQEFYETTLEALKDAK.DRLW.KTNTKLGKLYLE..
Retrocopy YLECSYTRNYSEKSINSILDYISTSK----HLDLLQEFYETTLEALKDAKTDRLWLKTNTKLGKLYLECE

Parental  EYGKLQKIXXXXXXXXXTDDGEDDLKKGTQLLEIY-ALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPL
          EYGKLQKI.........TD..EDDLKKGTQ.L.I........YTAQK.NKKLKALYEQSLHIKSAIPHPL
Retrocopy EYGKLQKILLQLHQSCKTDE-EDDLKKGTQ*LKIE>STTLELYTAQKTNKKLKALYEQSLHIKSAIPHPL

Parental  IMGVIRECGGKMHLREGEFEKAHTDFF-EAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAKP
          IMGVIRECG.KMH.REGEFEKAHT....E.FKNYDE.GSPR..TCLKYLVLANMLMKSGI.P.DSQ.A..
Retrocopy IMGVIRECGDKMHFREGEFEKAHTXXX>EVFKNYDEWGSPR*ITCLKYLVLANMLMKSGITPSDSQ-ARL

Parental  YKNDPEILAMTNLVSAYQNNDITEFEKILKT-NHSNIMDDPFIREHIEELLRNIRTQVLIKLIKPYTRIH
          Y.NDPEILAM.NLVSAYQNNDITEFEKILK..NHSNIMDD.FIREHIEE.L.N.RTQV.IKLIKPYTRIH
Retrocopy YRNDPEILAMMNLVSAYQNNDITEFEKILKK<NHSNIMDDLFIREHIEEVLQNTRTQVVIKLIKPYTRIH

Parental  IPFISKXXXXXXXXXXXXXXXXXXXXTIHGRIDQVNQLLELDHQKRGGARYTALDKWTNQLNSLNQAVVS
          IPFISK....................T.HG.IDQVNQLLELDH.KRGGA.YTALDKWT.QLNSLNQAVVS
Retrocopy IPFISKELNIDVADVESLLVECILDNTVHG*IDQVNQLLELDHLKRGGA*YTALDKWTTQLNSLNQAVVS

Parental  KLA
          KLA
Retrocopy KLA

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1288 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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,