RetrogeneDB ID: retro_tbel_4054

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_60335:414..849(-)
• 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_4054
TGCAACCAAATGATTCCAGGAAATAAGTATTTCTACCATATGAATAAATGTTGTCCAACCTCAGAGTTTGTGAATGATTT
TCCACCTGGAAAGTCAAAAACACCTTCACCATCCTTCCCAAGTCAGGCTGCTAAAAATCAGACTTCCACAGCATAGAAGG
ATGTCTGCCCAAAGACAAAAAATATGAACAGATTTCCTCTTCTTTATGAAAGTTCAACAAAGCAAGCACCAAGAGGCAAA
AACAAAGCCACAAATCTGCCTTCAAAGTCTGAGTTCAATCCTTGGGCCCCCTCTCCTACAGAAGATGAGGCAGCTTATAA
CATTCTGAGATGATGTTCCCAGTGTGGAATCCTGCTTCCCCTGTCAACTCTCACTCAGCATCAGGAGAAATGCCAGCAGT
TAGCTTCATTGAAAGCTAAACAAGTGAAAAATCTC

Alignment

ORF - retro_tbel_4054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.9 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CNQMIPGNKYFYHMKKC-PTSEFVNDFPPGKPKTPSPSFPSQAAKNQTSTAEKDVRPKTKNMNRFPLLYE
          CNQMIPGNKYFYHM.KC.PTSEFVNDFPPGK.KTPSPSFPSQAAKNQTSTA.KDV.PKTKNMNRFPLLYE
Retrocopy CNQMIPGNKYFYHMNKCCPTSEFVNDFPPGKSKTPSPSFPSQAAKNQTSTA*KDVCPKTKNMNRFPLLYE

Parental  SSTKQAPRGKNKAKNLPSKSEFNPWARSPTENEAAYNILRRCSQCGILLPLPTLTQHQEKCQRLASESTS
          SSTKQAPRGKNKA.NLPSKSEFNPWA.SPTE.EAAYNILR.CSQCGILLPL.TLTQHQEKCQ.LAS....
Retrocopy SSTKQAPRGKNKATNLPSKSEFNPWAPSPTEDEAAYNILR*CSQCGILLPLSTLTQHQEKCQQLASLKAK

Parental  EKSQL
          ....L
Retrocopy QVKNL

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_4054 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4054 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,