RetrogeneDB ID: retro_tbel_4497

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_86154:713..1427(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSTBEG00000008306
• Aliases: None
• Description: COP9 signalosome subunit 2 [Source:HGNC Symbol;Acc:30747]

Sequence

>retro_tbel_4497
ACAGCACAGAAAAATACCAAAACTTTAAAGCACTCTATGAACAGTCACTTCACATCAAGTCTGCCATCTCTCATCCACTG
ATCATGGGAGTCATCAGAGAATGTGGTGGTAAAATGCACTTGAGAGAAGGTGAATTTGAAAAGGCACACACTGATTTTTT
TTTGAAGCTTTAAAGAATTATGATGTATCAGAAGTCCGAGACGAACCACTTGCTTAAAATATTTGGTCTTAACAAATACG
CTAATGAAATCGGGAATAAATCCATTTGACTCGCAGGAGGCCAAACCATACAAGAATGATCCAGAAATTCTTGCAATGAC
AAATCTAGTAAGTGCCTATCAGAATAATGACATCACTGAATTTGAAAAGATTCTGAAAACAAATCACAGCAACATCATGG
ACGATCCCTTCATAAGAGAACACATTGAAGAACTTTTGCGAAACATCAGAACACAAGTGCTCATAAAATTAACTAAGCCT
TACACAAGAATACATATTCCTTTTATTTCTAAGGAGTTAAACATAGATGTAGCTGATGTGGAGAGCTTGCTGGTGCAGTG
CATATTGGATAACACTATTCATGGACGAATTGATCAAGTCAACCAACTCCTTGAACTAGATCATCAGAAGAGGGGTGGTG
CATGATATACTGCACTAGATAAATGGACCAATCAACCAAATTCTCTCAACCAGGCTGTAGTCAGTAAACTGGCT

Alignment

ORF - retro_tbel_4497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.24 %
• Parental protein coverage: 55.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TAQKNNKKL-KALYEQSLHIKSAIPHPLIMGVIRGKFECGGKMHLREGEFEKAHT-DFFEAFKNYDESGS
          TAQKN.K.L.KALYEQSLHIKSAI.HPLIMGVIR...ECGGKMHLREGEFEKAHT......FK......S
Retrocopy TAQKNTKTL<KALYEQSLHIKSAISHPLIMGVIR---ECGGKMHLREGEFEKAHT>XXXXSFKEL*CIRS

Parental  PRRTTCLKYLVLANMLMKSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDD
          PRRTTCLKYLVL.N.LMKSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDD
Retrocopy PRRTTCLKYLVLTNTLMKSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDD

Parental  PFIREHIEELLRNIRTQVLIKLIKPYTRIHIPFISKELNIDVADVESLLVQCI--DTINGQIDQANQLLE
          PFIREHIEELLRNIRTQVLIKL.KPYTRIHIPFISKELNIDVADVESLLVQCI...TI.G.IDQ.NQLLE
Retrocopy PFIREHIEELLRNIRTQVLIKLTKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLE

Parental  LDHQKRGGAQYTALDKWTNQLNSPNQAVVSKLA
          LDHQKRGGA.YTALDKWTNQ.NS.NQAVVSKLA
Retrocopy LDHQKRGGA*YTALDKWTNQPNSLNQAVVSKLA

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4497 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4497 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 11 parental genes, and 19 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	ENSTBEG00000001962	1 retrocopy	retro_tbel_1610,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497 ,
Tursiops truncatus	ENSTTRG00000000462	1 retrocopy	retro_ttru_328,