RetrogeneDB ID: retro_tbel_2620

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_114218:43299..44075(+)
• 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_2620
ATGGAGGGAACTTTCCAGGCGTGCGGGAACTGCAAAAGAAGTGTGCCTTCTTCCCACTTCACCCTCCATGAGGCCCACTG
CCTGCGCTTCCGAGAAGTGAAGGAGCATTGCATGAACCACCCCCCGCAGGCCAAGGAACACCAAGAGCGCCCAGCGGAGT
GCAAGTTCTGCGAGGTGGCTATTAGCCTCAGCAAGCTAGAGCTCCGCGAACAGCACTGTGGGGACCACATGGGGCTCTGC
TCAGACTGTAGTCAGCCTGTCAAGCTCCATGCGCTGGCCCAGCACAAAGATGTCTACCAGGGTGAACAAGCCCAGCTGGG
GGAAGGGAAGAAAAGTTTAGACTCTGAAAAGGAATCTACTGTTATGACTGCAACCAAATGATTCCAGGAAATAAGTATTT
CTACCATATGAATAAATGTTGTCCAACCTCAGAGTTTGTGAATGATTTTCCACCTGGAAAGTCAAAAACACCTTCACCAT
CCTTCCCAAGTCAGGCTGCTAAAAATCAGACTTCCACAGCAGAGAAGGATGTCCGCCCAAAGACAAAAAATATGAACAGA
TTTCCTCTTCTTTATGAAAGTTCAACAAAGCAAGCCCCAATAGGCAAAAACAAAGCCACGAATCTGCCTTCAAAGTCTGA
GTTCAATCCTTGGGCCCCCTCTCCTACAGAAGATGAGGCAGCTTATAACATTCTGAGATGATGTTCCCAGTGTGGAATCC
TGCTTCCCCTGTCAACTCTCACTCAGCATCAGGAGAAATGCCAGCAGTTAGCTTCA

Alignment

ORF - retro_tbel_2620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.77 %
• Parental protein coverage: 91.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGTFQVCGNCKRSVPSSHFTLHEAHCLRFREVKEHCMN--PQAEEHQERPAECKFCEVAMSLSKLELHE
          MEGTFQ.CGNCKRSVPSSHFTLHEAHCLRFREVKEHCMN..PQA.EHQERPAECKFCEVA.SLSKLEL.E
Retrocopy MEGTFQACGNCKRSVPSSHFTLHEAHCLRFREVKEHCMNHPPQAKEHQERPAECKFCEVAISLSKLELRE

Parental  QHCGGRMGLCPDCNQPVKLHALAQHKDVCQGEQAQLGEGKKNLDSEKE-IYCYYCNQMIPGNKYFYHMKK
          QHCG..MGLC.DC.QPVKLHALAQHKDV.QGEQAQLGEGKK.LDSEKE.IYCY.CNQMIPGNKYFYHM.K
Retrocopy QHCGDHMGLCSDCSQPVKLHALAQHKDVYQGEQAQLGEGKKSLDSEKE<IYCYDCNQMIPGNKYFYHMNK

Parental  C-PTSEFVNDFPPGKPKTPSPSFPSQAAKNQTSTAEKDVRPKTKNMNRFPLLYESSTKQAPRGKNKAKNL
          C.PTSEFVNDFPPGK.KTPSPSFPSQAAKNQTSTAEKDVRPKTKNMNRFPLLYESSTKQAP.GKNKA.NL
Retrocopy CCPTSEFVNDFPPGKSKTPSPSFPSQAAKNQTSTAEKDVRPKTKNMNRFPLLYESSTKQAPIGKNKATNL

Parental  PSKSEFNPWARSPTENEAAYNILRRCSQCGILLPLPTLTQHQEKCQRLAS
          PSKSEFNPWA.SPTE.EAAYNILR.CSQCGILLPL.TLTQHQEKCQ.LAS
Retrocopy PSKSEFNPWAPSPTEDEAAYNILR*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_2620 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2620 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,