RetrogeneDB ID: retro_tbel_2528

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_112566:39702..40350(+)
• 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_2528
TCATACATAGAAAATGCCAAACAGATTGGCCGCCTTGAAAATGCAATTGGCTGGTACCACAGTCACCCTGGCTATGGCTG
TTGGCTTTCTGGAATTGATGTTAGTACTCAGATGTTCAATCAGCAGTTCCAAGAACCATTTGTAGCAGTGGTCATTGATC
CAACAAGAACAATCTGTGCAGGGAAAGTGAATCTTGGAGGCTTTAGGTCATACCCAAAGGGCTACAAACCTCCCAATGAA
GGACCTTCTGAGTACCAGACTATCCCACTTAATAAAATAGAAGACTTCAGTGTACACTGCAAACAATATTATGCCTTAGA
AGTTTCATATTTCAAATCCTCCTTGGATCGCCAATTGCTTGAACTTTTGTGGAATAAATACTGGATGAATACGCTGAGTT
CTTCTAGTTTGCTTACTAATGCAGACTACACCCCCAGTCAGATCATTGATTTGTCTGAAAAGTTAGAGCAGTCAGAAGCT
CAGCTGGGACGGGGGAGTTTCATGTTGGGTTTAGAAACACATGACTGAAAATCAGAAGACAAACTTGCCAAAGCTACAAG
AGACAACTGTAAAACTACCATAGAAGCTATCCATGGATTGATGTCTCAAGTTATTAAGGATATATTGTTTAATCAAATTA
ATCTCTCT

Alignment

ORF - retro_tbel_2528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 65.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYIENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRT
          .YIENAKQ.GRLENAIGWYHSHPGYGCWLSGIDVSTQM.NQQFQEPFVAVVIDPTRTI.AGKVNLG.FR.
Retrocopy SYIENAKQIGRLENAIGWYHSHPGYGCWLSGIDVSTQMFNQQFQEPFVAVVIDPTRTICAGKVNLGGFRS

Parental  YPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLTN
          YPKGYKPP.EGPSEYQTIPLNKIEDF.VHCKQYYALEVSYFKSSLDR.LLELLWNKYW.NTLSSSSLLTN
Retrocopy YPKGYKPPNEGPSEYQTIPLNKIEDFSVHCKQYYALEVSYFKSSLDRQLLELLWNKYWMNTLSSSSLLTN

Parental  ADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKLAKATRDSCKTTIEAIHGLMSQVIKDKLF
          ADYT..Q..DLSEKLEQSEAQLGRGSFMLGLETHD.KSEDKLAKATRD.CKTTIEAIHGLMSQVIKD.LF
Retrocopy ADYTPSQIIDLSEKLEQSEAQLGRGSFMLGLETHD*KSEDKLAKATRDNCKTTIEAIHGLMSQVIKDILF

Parental  NQINIS
          NQIN.S
Retrocopy NQINLS

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_2528 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2528 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,