RetrogeneDB ID: retro_tbel_1082

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3787:310559..311336(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XAF1
• Ensembl ID: ENSTBEG00000008553
• Aliases: None
• Description: XIAP associated factor 1 [Source:HGNC Symbol;Acc:30932]

Sequence

>retro_tbel_1082
ATTGAGGGAACTTTCCAGGTGTGCGGGAACTGCAAAAGAAGTGTGCCTTCTTCCCACTTCACCCTCCATGAGGCCCACTG
CCTGCGCTTCCGAGAAGTGAAGGAGCATTGCATGAACCACCCCCCGCAGGCCAAGGAACACCAAGAGCGCCCGGCGGAGT
GCAAGTTATGCGAGGTGGCTATTAGCCTCAGCAAGCTGGAGCTCCGCGAACAGCACTGTGGGGACCACATGGGGCTCTGC
TCAGACTGTAATCAGCCTGTCAAGCTCCACGCCCTGGCCCAGCACAAAGATGTCTACCAGGGTGAACAAGCCCAGCTGGG
GGAAGGGAAGAAAAGTTTAGACTCTGAAAAGGAAATCTACTGTTATGACTGCAACCAAATGATTCCAGGAAATAAGTATT
TCTACCATATGAATAAATGTTGTCCAACCTCAGAGTTTGTGAATGATTTTCCACCTGGAAAGTCAAAAACACCTTCACCA
TCCTTCCCAAGTCAGGCTGCTAAAAATCAGACTTCCACAGCAGAGAAGGATGTCCGCCCAAAGACAAAAAATATGAACAG
ATTTCCTCTTCTTTATGAAAGTTCAACAAAGCAAGCCCCAACAGGCAAAAACAAAGCCACGAATCTGCCTTCAAAGTCTG
AGTTCAATCCTTGGGCCCCCTCTCCTACAGAAGATGAGGCAGCTTATAACATTCTGAGATGATGTTCCCAGTGTGGAATC
CTGCTTCCCCTGTCAACTCTCACTCAGCATCAGGAGAAATGCCAGCAGTTAGCTTCA

Alignment

ORF - retro_tbel_1082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.12 %
• Parental protein coverage: 91.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGTFQVCGNCKRSVPSSHFTLHEAHCLRFREVKEHCMN--PQAEEHQERPAECKFCEVAMSLSKLELHE
          .EGTFQVCGNCKRSVPSSHFTLHEAHCLRFREVKEHCMN..PQA.EHQERPAECK.CEVA.SLSKLEL.E
Retrocopy IEGTFQVCGNCKRSVPSSHFTLHEAHCLRFREVKEHCMNHPPQAKEHQERPAECKLCEVAISLSKLELRE

Parental  QHCGGRMGLCPDCNQPVKLHALAQHKDVCQGEQAQLGEGKKNLDSEKEIYCYYCNQMIPGNKYFYHMKKC
          QHCG..MGLC.DCNQPVKLHALAQHKDV.QGEQAQLGEGKK.LDSEKEIYCY.CNQMIPGNKYFYHM.KC
Retrocopy QHCGDHMGLCSDCNQPVKLHALAQHKDVYQGEQAQLGEGKKSLDSEKEIYCYDCNQMIPGNKYFYHMNKC

Parental  -PTSEFVNDFPPGKPKTPSPSFPSQAAKNQTSTAEKDVRPKTKNMNRFPLLYESSTKQAPRGKNKAKNLP
          .PTSEFVNDFPPGK.KTPSPSFPSQAAKNQTSTAEKDVRPKTKNMNRFPLLYESSTKQAP.GKNKA.NLP
Retrocopy CPTSEFVNDFPPGKSKTPSPSFPSQAAKNQTSTAEKDVRPKTKNMNRFPLLYESSTKQAPTGKNKATNLP

Parental  SKSEFNPWARSPTENEAAYNILRRCSQCGILLPLPTLTQHQEKCQRLAS
          SKSEFNPWA.SPTE.EAAYNILR.CSQCGILLPL.TLTQHQEKCQ.LAS
Retrocopy SKSEFNPWAPSPTEDEAAYNILR*CSQCGILLPLSTLTQHQEKCQQLAS

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_1082 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1082 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 1 parental gene, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000008553	5 retrocopies	retro_tbel_1082 , retro_tbel_2541, retro_tbel_2620, retro_tbel_4054, retro_tbel_952,