RetrogeneDB ID: retro_tbel_3896

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_2981:28720..29264(-)
• 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_3896
ATCCTAATGGCAAAGTACTGGACTAAGGATCACCATTAGTTTAAATATTGAAAAATCTCAGCATTGATTCTACTGAAAAT
GGTGATGTATGACAGATCAGAAGGCAATTTGGGAAGTGATGGGTTTGATGCTAGGGAAGGTGGACAGTGAAACCATGATC
ATTATGGATAGTTTTGCTTTACCTGTACAGGGCACTGAAACCTGAGTAAATGCTCAGGCTGCTGCCTGTGAGTACATGGC
TGCATACACAGAAAATGCTGAACAGGTTGACTGCCTGTAAAATGCAATTTGCTGGTATCACAGCCACCCTGGCTGTGGTT
GCTGGCTTTCTGAAATTGAAGTTACTACTCAGATATTCAATCAGCAGTTCCAAGAACCATTTGTAGCAGTGGTAATTGAT
CCAGTAAGAACAATCGCTGCAGGGAAAGTGAATCTTGGAGCCTTTAGGACATACCCAAAGAGTTACAAACCTCCTAATGA
AAGACCTTCAGAATACCAGACTATGTCACTTAATAAAATAGAAAACATTGGTGTACATTGTAAA

Alignment

ORF - retro_tbel_3896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 54.52 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILAAKPGTKDHHYFKYCKISALALLKMVMHARSGGNL-EVMGLMLGKVDGETMIIMDSFALPVEGTETRV
          IL.AK..TKDHH.FKY.KISAL.LLKMVM..RS.GNL.EVMGLMLGKVD.ETMIIMDSFALPV.GTET.V
Retrocopy ILMAKYWTKDHH*FKY*KISALILLKMVMYDRSEGNL>EVMGLMLGKVDSETMIIMDSFALPVQGTET*V

Parental  NAQAAAYEYMAAYIENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTIS
          NAQAAA.EYMAAY.ENA.QV..L.NAI.WYHSHPG.GCWLS.I.V.TQ..NQQFQEPFVAVVIDP.RTI.
Retrocopy NAQAAACEYMAAYTENAEQVDCL*NAICWYHSHPGCGCWLSEIEVTTQIFNQQFQEPFVAVVIDPVRTIA

Parental  AGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCK
          AGKVNLGAFRTYPK.YKPP.E.PSEYQT..LNKIE..GVHCK
Retrocopy AGKVNLGAFRTYPKSYKPPNERPSEYQTMSLNKIENIGVHCK

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_3896 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3896 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,