RetrogeneDB ID: retro_tbel_3925

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_39396:269..832(+)
• 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_3925
TTTAACTTGAATTCTCTCTTGGTGGGTCTAGAATTAATATCAGATACATACCTTGCACTTTTCTTGGCTCAGCTGCAACA
GGAACGTTATTCTATATTTGTCATCAAGGGTGATCTGCTGGATTGTGAAGCTGACCAACTCCTACAGATGATCAGGGTCC
AACAAACGCATCAACCAAAACTTACTGGATAAGAATTAGCACAACTAAAAGATCAGAGAGTCCATAAAATAGACCTAGAA
TGAATCTTAGAAGCAAATCATGGGTCAGGAATGTTAGACGAAGATGAGGAGGATTTGCAGAGGGCCCTGGCACTAAGTCA
CCAAGAAATTGACATGGAGGATGAAGAAGCAAATCTCCACAGGGCTATTCAGCTCAGTATGCAAAGTAGTTCCAGAAATA
TATCTCAAGGTAGTCCACAGACATCAAGCACAAATCTTACTTCAGAAGAGTTGCGGAAGAGAAGCCTACTTTGAAAAGCA
GCAGCAGCCAGATCCACCAGGACAGGTCTCCTGTCCATGTGGAAGGAGCACTTGGGAACGATCCAGGTGATGATGCTATG
AGT

Alignment

ORF - retro_tbel_3925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.6 %
• Parental protein coverage: 53.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLK
          FNLNSLL.G.ELISDTYLALFLAQLQQE.YSIFV.KGDL.DCEADQLLQMIRVQQ.H.PKL.G.ELAQLK
Retrocopy FNLNSLLVGLELISDTYLALFLAQLQQERYSIFVIKGDLLDCEADQLLQMIRVQQTHQPKLTG*ELAQLK

Parental  DQRVHKTDLERVLEANDGSGMLDEDEEDLQRALALSRQEIDMEDEEADLRRAIQLSMQGSSRNISQDSPQ
          DQRVHK.DLE..LEAN.GSGMLDEDEEDLQRALALS.QEIDMEDEEA.L.RAIQLSMQ.SSRNISQ.SPQ
Retrocopy DQRVHKIDLE*ILEANHGSGMLDEDEEDLQRALALSHQEIDMEDEEANLHRAIQLSMQSSSRNISQGSPQ

Parental  MSSTNLTSEELRKR-REAYFEKQQQQHQQQQQQQPPGQVSHPCGKPTTS
          .SSTNLTSEELRKR..........Q.HQ........G......G....S
Retrocopy TSSTNLTSEELRKR<KPTLKSSSSQIHQDRSPVHVEGALGNDPGDDAMS

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_3925 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3925 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 ,