RetrogeneDB ID: retro_tbel_1073

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3760:358728..358968(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBCA
• Ensembl ID: ENSTBEG00000006034
• Aliases: None
• Description: tubulin folding cofactor A [Source:HGNC Symbol;Acc:11579]

Sequence

>retro_tbel_1073
TTGGTCATAGAAAAGGTGATGTATGAAAATGAAGCAAAAACAACAAAACTGGGGAAAAAAAAAAAAAAAAAAAGCTGAAG
GTGGTGAAAATTAGGCCATTAAAAAGCAGGCTGAGATCCTGAAGAAGCCCCAGTTGATGACCCCCGATTGCCAGTGCAGG
TTGGAAGCTGTACATACGGATCTCCAACAGGTACTAGGAAATGAAAATATGTGGAAGATGCTCAAAAACATAAAGAAGCA

Alignment

ORF - retro_tbel_1073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.32 %
• Parental protein coverage: 87.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVKEKAMYEKEA-KQQE-EKIEKMKAEDGENYAIKKQAEILQESGMMIPDCQ-RREAAYTVLQQILENE-
          LV.EK.MYE.EA.KQQ.........AE.GEN.AIKKQAEIL.....M.PDCQ.R.EA..T.LQQ.L.NE.
Retrocopy LVIEKVMYENEA>KQQNWXXXXXXXAEGGEN*AIKKQAEILKKPQLMTPDCQCRLEAVHTDLQQVLGNE<

Parental  KDLEEAEEYKEA
          K..E.A...KEA
Retrocopy KYVEDAQKHKEA

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_1073 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1073 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 12 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014223	4 retrocopies	retro_acar_11, retro_acar_130, retro_acar_142, retro_acar_195,
Callithrix jacchus	ENSCJAG00000019848	4 retrocopies	retro_cjac_114, retro_cjac_2160, retro_cjac_2173, retro_cjac_2974,
Cavia porcellus	ENSCPOG00000012187	1 retrocopy	retro_cpor_930,
Echinops telfairi	ENSETEG00000016572	1 retrocopy	retro_etel_93,
Macaca mulatta	ENSMMUG00000011853	1 retrocopy	retro_mmul_229,
Mus musculus	ENSMUSG00000042043	3 retrocopies	retro_mmus_1486, retro_mmus_2839, retro_mmus_2970,
Ochotona princeps	ENSOPRG00000002460	4 retrocopies	retro_opri_550, retro_opri_727, retro_opri_879, retro_opri_91,
Rattus norvegicus	ENSRNOG00000048342	1 retrocopy	retro_rnor_140,
Sorex araneus	ENSSARG00000009943	1 retrocopy	retro_sara_699,
Ictidomys tridecemlineatus	ENSSTOG00000009840	1 retrocopy	retro_itri_246,
Tupaia belangeri	ENSTBEG00000006034	6 retrocopies	retro_tbel_1073 , retro_tbel_113, retro_tbel_1286, retro_tbel_2336, retro_tbel_2905, retro_tbel_756,
Tarsius syrichta	ENSTSYG00000000514	1 retrocopy	retro_tsyr_1038,