RetrogeneDB ID: retro_tbel_435

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_208:329622..330109(-)
• Located in intron of: ENSTBEG00000011301

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2B
• Ensembl ID: ENSTBEG00000015927
• Aliases: None
• Description: transformer 2 beta homolog (Drosophila) [Source:HGNC Symbol;Acc:10781]

Sequence

>retro_tbel_435
TCCAGAAGTGTAAGTTCTCAGGGATCAGGGAAATCTGCAAGGTATAGCCCTGCAAGCCCTCCATCGAGGAAGATTACAGG
TGGTCTAGATCAAAGTCTAGGTCCAGACTGAATCTAGATCTAGATACAGAAGAAGCGCTGGAAGTCGCTATACAAGGTCC
GGGCTATGGCCTCCCTCCCATAGGCAACCCTGTGGCAGAATTTATAGTCGAGGTTATTGAAGAGGACACAGTCACTCTCC
CATGTCTACTAGCAGGTGCCATGTTGGGAAACAGGCAAATCCTGATCCCAACTGTTTTCTTGGAGTATTTGGGTTGAGCT
TGTACACCACAGAAAGAGATCTAAGAGAAGTATTCTCTAAATATAGCCCCTTGGCTGATGTGTCTACTGTGTATGACCAA
TCGTTTAAGCAGTTGAGAGGATTTGCCTTTGTGTATTTTGAAAGTGTAGGTGATGCCGAGGAACCTGCCAACAGGATGGA
GCTTGAT

Alignment

ORF - retro_tbel_435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.47 %
• Parental protein coverage: 60.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRSGSAHGSGKSARHTPARSRSK-EDSRRSRSKSRSR-SESRSRSRRSSRRHYTRSRSRSRSHRRSRSRS
          SRS.S..GSGKSAR..PA...S..ED.R.SRSKSRSR..ESRSR.RRS....YTRS.....SHR....R.
Retrocopy SRSVSSQGSGKSARYSPASPPSR<EDYRWSRSKSRSR<TESRSRYRRSAGSRYTRSGLWPPSHRQPCGRI

Parental  YSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQS
          YSR.Y.R...HSHSPMST.R.HVG..ANPDPNC.LGVFGLSLYTTERDLREVFSKY.P.ADVS.VYDQ..
Retrocopy YSRGY*R--GHSHSPMSTSRCHVGKQANPDPNCFLGVFGLSLYTTERDLREVFSKYSPLADVSTVYDQSF

Parental  RRSRGFAFVYVDD-KEAKERANGMELD
          ...RGFAFVY......A.E.AN.MELD
Retrocopy KQLRGFAFVYFESVGDAEEPANRMELD

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_435 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_435 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tupaia belangeri	ENSTBEG00000015927	1 retrocopy	retro_tbel_435 ,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,