RetrogeneDB ID: retro_tbel_2719

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_117472:5628..6436(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSGALNACT2
• Ensembl ID: ENSTBEG00000012462
• Aliases: None
• Description: chondroitin sulfate N-acetylgalactosaminyltransferase 2 [Source:HGNC Symbol;Acc:24292]

Sequence

>retro_tbel_2719
GACATTACTGGATCAATTATTAATATCATCGTACCCCTTGCTGAAAGAACTCAAGCATTTGCACAATTTATGCAGAACTT
CAGGGATGTTTGTATTTATCAAGCCAAAAGGATTCATCTTACAGTGGTGTATTTTGGTAAAGAAGGATTGTCAAAGTGTC
CAGTCTATCCTAGAATCAGTCACAAGTGAGTCTAATTTTCATGATTATACCTTAGTCTCATTGAATGAAGAATTTAATCA
TGGATGAAGGCTAAATGTGGGTGCCTGAGCTTGGGACAAGGAAGAGGTCTTGATGTTTTCTTGTGATGTCGATATATATT
TCTCAGCTGAATTCCTTAAGAGTTACCAATAAAATGCTGAGCCAGGTAAGAAGGTGTTTTACCCTGTGGTGTTCAGCCTT
TACAATCCTGCCATTGTTTATGCCAACCAGAACGTGCCACCACCTGTAGAGAGTCAACTGGTTAACAAAAAGGATTCTGA
CTTTTGGTGAGATTTTGGCTTTAGGTTGACTTATCAATATTGATCAGATTTCCTGACTATTGGTGGATTTGACATGAAAG
TGAAAGTTTGCGGTAGAGAAGATGTTCATCTTTATAGAAAATACTTACATGGTGACCTTATAGTGGTTTGAATTCCAGTT
CCTGGTCTTTTCCATCTCTTGCATGAACAGTACTGTGCTGATAAGCAGTACCACACGTGTATACAGTCCAAAGTCATGAA
CAAGGCCTCTCACTCCCACGTGGGGATGCTGGTCTTCAGAGAGGAAATAGAGACGCATCTTCATAAACAGGCATACAGCA
CAACAAAC

Alignment

ORF - retro_tbel_2719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 50.37 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DITRSIINIIVPLAERTEAFAQFMQNFRDVCIHQDKRIHLTVVYFGKEGLSK-VKSILESVTSESNFHNY
          DIT.SIINIIVPLAERT.AFAQFMQNFRDVCI.Q.KRIHLTVVYFGKEGLSK.V.SILESVTSESNFH.Y
Retrocopy DITGSIINIIVPLAERTQAFAQFMQNFRDVCIYQAKRIHLTVVYFGKEGLSK>VQSILESVTSESNFHDY

Parental  TLVSLNEEFNRGRGLNVGARAWDKGEVLMFFCDVDIYFSAEFLNSCRLNAEPGKKVFYPVVFSLYNPAIV
          TLVSLNEEFN.G..LNVGA.AWDK.EVLMF.CDVDIYFSAEFL.S...NAEPGKKVFYPVVFSLYNPAIV
Retrocopy TLVSLNEEFNHG*RLNVGA*AWDKEEVLMFSCDVDIYFSAEFLKSYQ*NAEPGKKVFYPVVFSLYNPAIV

Parental  YANQDVPPPVEQQLVHKKDSGFWRDFGFGMTCQYRSDFLAIGGFDMEVKGWGGEDVHLYRKYLHGDLIVV
          YANQ.VPPPVE.QLV.KKDS.FW.DFGF..T.QY.SDFL.IGGFDM.VK..G.EDVHLYRKYLHGDLIVV
Retrocopy YANQNVPPPVESQLVNKKDSDFW*DFGFRLTYQY*SDFLTIGGFDMKVKVCGREDVHLYRKYLHGDLIVV

Parental  RTPVPGLFHLWHEKRCADELTPEQYRMCIQSKAMNEASHSHLGMLVFREEIETHLHKQAYRTNS
          ..PVPGLFHL.HE..CAD.....QY..CIQSK.MN.ASHSH.GMLVFREEIETHLHKQAY.T..
Retrocopy *IPVPGLFHLLHEQYCAD----KQYHTCIQSKVMNKASHSHVGMLVFREEIETHLHKQAYSTTN

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_2719 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2719 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169826	1 retrocopy	retro_hsap_4732,
Pongo abelii	ENSPPYG00000002209	1 retrocopy	retro_pabe_3679,
Tupaia belangeri	ENSTBEG00000012462	2 retrocopies	retro_tbel_2719 , retro_tbel_4730,