RetrogeneDB ID: retro_tbel_3914

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_3637:83720..84722(-)
• 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_3914
ATGGTGGTGTCCAGGAGCCGTATGGCCCAGAAAACCTGGGAATTGGCCAACAACATGCAGGAAGCCCAGAGTATCGATGA
AATCTACAAGTATGACAAGAAACAGCAGCAAGAAATCTTAGCGGTGAAGCCCTGGACTAAGGATCACCATTACTTTAAGT
ACTGCAAAATCTCAGCATTGGCTCTACTAAAAATGGTGATGCATGCCAGATCAGGAGGCAACTTGGATGTGATGGGATTG
ATGCTAGGAAAGGTGGACGATGAAACCATGATCATTATGGACAGTTTTGCTTTGCCTGTAGAGGGCACTGAAACCCGAGT
AAATGCTCAGGCTGCTGCCTATGAATACATGGCTGCATACATAGAAAATGTCAAACAGGTTGGCTGCCTTGAAAATGCAA
TTGACTGGTACCACAGCCACCCTGGCTATGGCTACTGGCTTTCTGGAATTGATGTTAGTACTCAGATGCTCAATCAGCAG
TTCCAAGAACCATTTGTAGCAGTGGTCATTGATCCAACAAGAACAATCTCTGCAGGGAAAGTGAATCTTGGAGCCTTTAG
GACATACCCAAAGGGCTACAAACCTCCCAATGAAGGACCTTCTGAGTACCAGACTATCCTACTTAATAAAATAGAAGACT
TTGGTGTACACTGCAAACAATATTATGCCTTAGAAGTTTCATATTTCAAATCCTCATTGGATCGCAAATTGCTTGAACTT
TTGTGGAATAAATACTGGGTGAATACGCTGAGTTCCTCTAGTTTGCTTACTAATGCAGACTACACCACTGGTCAGATCTT
TGATTTGTCTGAAAAGTTAGAGCAGTCAGAAGCTCAGCTGGGATGGGGGAGTTTCATGTTGGGTTTAGAGACACATGACC
GAAAATCAAAAGACAAACTTGCCAAAGCTACAAGAGACAGCTGTAAAACTACCATAGGAGCTATCCATGGATTGATGTCT
CAAGTTATTAAGGATAAATTGTTTAATCAAATTAATATCTCT

Alignment

ORF - retro_tbel_3914 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQG--ILAAKPGTKDHHYFKYCKISALALLKMVMHAR
          M..S.S.MAQKTWELANNMQEAQSIDEIYKYDKKQ...ILA.KP.TKDHHYFKYCKISALALLKMVMHAR
Retrocopy MVVSRSRMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAVKPWTKDHHYFKYCKISALALLKMVMHAR

Parental  SGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSH
          SGGNL.VMGLMLGKVD.ETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIEN.KQVG.LENAI.WYHSH
Retrocopy SGGNLDVMGLMLGKVDDETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENVKQVGCLENAIDWYHSH

Parental  PGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNK
          PGYG.WLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPP.EGPSEYQTI.LNK
Retrocopy PGYGYWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPNEGPSEYQTILLNK

Parental  IEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQL
          IEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLTNADYTTGQ.FDLSEKLEQSEAQL
Retrocopy IEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLTNADYTTGQIFDLSEKLEQSEAQL

Parental  GRGSFMLGLETHDRKSEDKLAKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
          G.GSFMLGLETHDRKS.DKLAKATRDSCKTTI.AIHGLMSQVIKDKLFNQINIS
Retrocopy GWGSFMLGLETHDRKSKDKLAKATRDSCKTTIGAIHGLMSQVIKDKLFNQINIS

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_3914 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3914 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 ,