RetrogeneDB ID: retro_tbel_2635

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_114895:238666..239340(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN3
• Ensembl ID: ENSTBEG00000008099
• Aliases: None
• Description: ataxin 3 [Source:HGNC Symbol;Acc:7106]

Sequence

>retro_tbel_2635
TGGTTTACCTTGAATTCTCTCTTGATGGGTCCAGAATTAATATTGGATACATACTTGCACTTTTCTTGGCTCAGTTACAA
CTGAAAAGTTATTCTATATTTGTTGTTAAGGGTGATCTGCAGGATTGTGAAGATGACCAACTCCTACAGATGATCAGGAG
CCAACAGATGCATCTACCAAAATTCTTATTGGAGAATTAGCACAACAGAAAGATCAGAGAATCCATAAAACAGACCTGGA
ACAAGTCTTAGAAGCAAATGATGGGTCCGGAATGTTAGAGGAAGATAAACAGGATTTGCAGAGGGCTCTAGCACTAAGTT
GTCAAGAAATTGACATGGAAGATGAAGAAGCAGATCTCCACTGGCTATTCAGCTCAGTAAGCAAGGCAGTTCCAGAAATA
TATCTGGAACTATTCCACAGACATCAAGCACATATCTTGCTTCAGAAGAGCTGCAGAAGAGAAAGAGAAGCCTACTTTTG
AAAAGCAACAGCAGTAGCTGCAGCAGGGAGATCCACAAGGACAGATCTTCTATCCATGTGGAAGGCCGACCACAAGGTCA
GACGCACTTGGGAATGATCGAGGTGATGATGCGATGAGTGAAGACGTGCTTCAGGCAGCTGCGATCATGTCTTTGGAAAC
TGTTACAAATAGTTTGAAAACAGAATGAAAGAAA

Alignment

ORF - retro_tbel_2635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.79 %
• Parental protein coverage: 65.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  WFNLNSLLTGPELISDTYL-ALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGE-ELA
          WF.LNSLL.GPELI.DTYL.ALFLAQLQ...YSIFVVKGDL.DCE.DQLLQMIR.QQMH.PK...E.ELA
Retrocopy WFTLNSLLMGPELILDTYL<ALFLAQLQLKSYSIFVVKGDLQDCEDDQLLQMIRSQQMHLPKFLLE<ELA

Parental  QLKDQRVHKTDLERVLEANDGSGMLDEDEEDLQRALALSRQEIDMEDEEADLR-RAIQLSMQGSSRNISQ
          Q.KDQR.HKTDLE.VLEANDGSGML.ED..DLQRALALS.QEIDMEDEEADL...AIQLS.QGSSRNIS.
Retrocopy QQKDQRIHKTDLEQVLEANDGSGMLEEDKQDLQRALALSCQEIDMEDEEADLH<LAIQLSKQGSSRNISG

Parental  DSPQMSSTNLTSEELRKR-REAY-FEKQQQQHQQQQQQQPPGQVSHPCGKPTTSSGAFGNDLGDDAMSEE
          ..PQ.SST.L.SEEL.KR.REAY.FEKQQQ..QQ.....P.GQ...PCG.PTT.S.A.GND.GDDAMS.E
Retrocopy TIPQTSSTYLASEELQKR>REAY>FEKQQQ*LQQ---GDPQGQIFYPCGRPTTRSDALGNDRGDDAMS-E

Parental  DMLQAAVTLSLETVRNNLKTEGKK
          D.LQAA...SLETV.N.LKTE.KK
Retrocopy DVLQAAAIMSLETVTNSLKTE*KK

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_2635 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2635 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005786	2 retrocopies	retro_btau_1652, retro_btau_330,
Choloepus hoffmanni	ENSCHOG00000005302	1 retrocopy	retro_chof_2238,
Callithrix jacchus	ENSCJAG00000018025	2 retrocopies	retro_cjac_1724, retro_cjac_375,
Cavia porcellus	ENSCPOG00000010887	1 retrocopy	retro_cpor_1460,
Homo sapiens	ENSG00000066427	1 retrocopy	retro_hsap_89,
Macaca mulatta	ENSMMUG00000020751	1 retrocopy	retro_mmul_298,
Monodelphis domestica	ENSMODG00000002006	2 retrocopies	retro_mdom_1498, retro_mdom_1573,
Nomascus leucogenys	ENSNLEG00000017126	1 retrocopy	retro_nleu_66,
Pongo abelii	ENSPPYG00000006075	1 retrocopy	retro_pabe_9,
Tupaia belangeri	ENSTBEG00000008099	3 retrocopies	retro_tbel_102, retro_tbel_2635 , retro_tbel_3925,