RetrogeneDB ID: retro_tbel_4354

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_78146:6778..7534(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP2
• Ensembl ID: ENSTBEG00000016814
• Aliases: None
• Description: S-phase kinase-associated protein 2, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:10901]

Sequence

>retro_tbel_4354
AGGAAGCACCTCCAGGAGATGCTAGACCAGAGTAGCAATGTTACCACAAGTTTCATGTGGAGGTGGGATTCTAGCAAGAG
TTCTGAACTGCTGTCAGGCATGGGAGGTCTCTGCCCTGGAGAAGGAAGAAGTGGACAGTAAGAATATACCTCAAGAACTG
CTCTCAAACCTAGGCCACCCCAGAACCCCTCCCAGAAATGGGCAAAGAGCGAAGGGAATGACAAAGACTTTATGATTGTC
TGCAGACCTAAGCTAAATCTAGAGAACTTTATAGGTGTGTCATGGGACTCCCTCCCCGATGAACTGCTCTTAGGGATCTT
TTCTTGTTTATGTCTCCTGAAACTGCTTAAAATCTCCCATGTTTGTAAAAGGTGGTATTACCTGGTGCTTGATGAGTCTC
TATGGCAGACCTTAGACTTTACAGGTAAAAATCTGCATCCAGATGTGATTGGTTGGTTGATGTCTTGAGGGGTGGTTGGC
TTTTGCTGTCCACAATCATTTATGGACCACCATTGGTTGAACATTTCAGCCCTTTTCACATTCAGCGCATGGACCTGTTG
AACTCGGTAATAGATGCGTCTACCCTCCACGGCATTCTGTCTTGGCATTTCAAATTGGAGAATCTAAGCCTGGAAGGTTT
ACAGCTTTTGAATCCCATTGTCAAAAATCTTGCTCAGAATTAAGATTTGTGTGACTAAACCTTAATGATGTTCCGGATTC
TCCGAATCTGCCCTGAAGTCTGTAAGTAGCTGTTCA

Alignment

ORF - retro_tbel_4354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.83 %
• Parental protein coverage: 58.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RKHLQEIPDQSSNVTTSFTWGWDSSKTSELLSGMG-VSALEKEEVDSENIPQELLSNLGQP-QSPSRKRL
          RKHLQE..DQSSNVTTSF.W.WDSSK.SELLSGMG.VSALEKEEVDS.NIPQELLSNLG.P.Q.PS.K..
Retrocopy RKHLQEMLDQSSNVTTSFMWRWDSSKSSELLSGMG>VSALEKEEVDSKNIPQELLSNLGHP<QNPSQKWA

Parental  KSKGNDKDFVIVRRPKLNRESFTGVSWDSLPDELLLGIFSCLCLPDLLKVSGVCKRWYCLVFDESLWQTL
          KS.GNDKDF.IV.RPKLN.E.F.GVSWDSLPDELLLGIFSCLCL..LLK.S.VCKRWY.LV.DESLWQTL
Retrocopy KSEGNDKDFMIVCRPKLNLENFIGVSWDSLPDELLLGIFSCLCLLKLLKISHVCKRWYYLVLDESLWQTL

Parental  DLTGKNLHPDVVGRLLSRGVIAFRCPRSFMDQ-PLVEHFSPFRVQHMDLSNSVIDVSTLQGILSQCFKLQ
          D.TGKNLHPDV.G.L.S.GV..F.CP.SFMD..PLVEHFSPF..Q.MDL.NSVID.STL.GILS..FKL.
Retrocopy DFTGKNLHPDVIGWLMS*GVVGFCCPQSFMDH<PLVEHFSPFHIQRMDLLNSVIDASTLHGILSWHFKLE

Parental  NLSLEGLRLSDPIVNNLAQNSNL-VRLNLCG-CSGFSEFALKTLLSSCS
          NLSLEGL.L..PIV.NLAQN..L.V.LNL...CSGFSE.ALK...SSCS
Retrocopy NLSLEGLQLLNPIVKNLAQN*DL<V*LNLND<CSGFSESALKS-VSSCS

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_4354 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4354 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525, retro_btau_555,
Choloepus hoffmanni	ENSCHOG00000006980	1 retrocopy	retro_chof_1604,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28,
Tupaia belangeri	ENSTBEG00000016814	1 retrocopy	retro_tbel_4354 ,