RetrogeneDB ID: retro_tbel_3147

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_131550:208819..209570(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS5
• Ensembl ID: ENSTBEG00000008440
• Aliases: None
• Description: COP9 signalosome subunit 5 [Source:HGNC Symbol;Acc:2240]

Sequence

>retro_tbel_3147
AAGATGGACAGTGAAACCATGATCATTATGGACAGTTTTGCTTTGCCTGTAGAGGGCACTGAAACCCGAGTAAATACTCA
GGCTGCTGCCTATGAGTAAATGGCTCCATACATAGAAAATGCCAAACAGCTTGGCCGCCTTGAAAATGCAATTGGCTGGT
ACCACAGCCACCCAGGCTATGGCTGCTGGCTTTCTGGAAATGATGTTAGTACTCAGATGCTCAATCAGCAGTTCCAAGAA
CCATTTGTAGCAGGGGTCATTGATCCAACAAGAACAATCTCTGCAGGAAAGTGAATCTTGGAGCCTATAGGACATACTCA
AAGGGCTACAAACCTCCCAATGAAGGACCTGCTGAGTACCAGACTATCCCATTTAATAAAATAGAAGACTTTGGTTACAC
TGCAAACAATATTATGCCTTAGAAGTTTCATATTTCGAATCTTCATTAGATCGCAAATTGCTTGAACTTTTGCAGAATAA
ATACTGGGTGAATACGCTGAGATCCTCTAGCTTGCTTACTAATGCAGACTATACCACGGGTCAGGTCTTTGATTTGTCTG
AAAAGTAAGAGCAGTCAGAAGTTCAGCTGAGATGGGGGAGTTTCATGTTGGGTTTAGAAACACATGACTGAAAATCAGAA
GACAAAATTGCCAAAGCTACAAGAGACAGCTGTAAAACTACCATAGAAGCTATCCATAGATTGATGTCTCAGGTTATTAA
GGATAAACTATTTAATCAAATTAATGTCTCT

Alignment

ORF - retro_tbel_3147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 75.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSHPGYGCWLSGIDVS
          K.D.ETMIIMDSFALPVEGTETRVN.QAAAYE.MA.YIENAKQ.GRLENAIGWYHSHPGYGCWLSG.DVS
Retrocopy KMDSETMIIMDSFALPVEGTETRVNTQAAAYE*MAPYIENAKQLGRLENAIGWYHSHPGYGCWLSGNDVS

Parental  TQMLNQQFQEPFVAVVIDPTRTISAGK-VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFG-VHCKQY
          TQMLNQQFQEPFVA.VIDPTRTISAGK.VNLGA.RTY.KGYKPP.EGP.EYQTIP.NKIEDFG..HCKQY
Retrocopy TQMLNQQFQEPFVAGVIDPTRTISAGK<VNLGAYRTYSKGYKPPNEGPAEYQTIPFNKIEDFG<LHCKQY

Parental  YALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLET
          YALEVSYF.SSLDRKLLELL.NKYWVNTL.SSSLLTNADYTTGQVFDLSEK.EQSE.QL..GSFMLGLET
Retrocopy YALEVSYFESSLDRKLLELLQNKYWVNTLRSSSLLTNADYTTGQVFDLSEK*EQSEVQLRWGSFMLGLET

Parental  HDRKSEDKLAKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
          HD.KSEDK.AKATRDSCKTTIEAIH.LMSQVIKDKLFNQIN.S
Retrocopy HD*KSEDKIAKATRDSCKTTIEAIHRLMSQVIKDKLFNQINVS

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_3147 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3147 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002028	1 retrocopy	retro_chof_556,
Callithrix jacchus	ENSCJAG00000004632	1 retrocopy	retro_cjac_2454,
Myotis lucifugus	ENSMLUG00000011697	1 retrocopy	retro_mluc_1528,
Monodelphis domestica	ENSMODG00000007838	1 retrocopy	retro_mdom_1460,
Mustela putorius furo	ENSMPUG00000010175	1 retrocopy	retro_mputfur_397,
Tupaia belangeri	ENSTBEG00000008440	7 retrocopies	retro_tbel_1083, retro_tbel_1833, retro_tbel_1853, retro_tbel_2528, retro_tbel_3147 , retro_tbel_3896, retro_tbel_3914,