RetrogeneDB ID: retro_tbel_4730

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_99256:21943..22850(+)
• 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_4730
ACACAATATGAACTCTTCTTCAAGAAAGCAGACCTTATGGATTATAGAAATGTAACCCACTTTCACCTTTTTGGACCTCT
CATGAAAATAAAGACTGAGATGATTGACATTACTGGATCAATTATTAATATCATTGTACCCCTTGCTGAAAGAACTCAAG
CATTTGCACAATTTATGCAGAACTTCAGGGATGTTTGTATTTATCAAGCCAAAAGGATTCATCTTACAGTGGTGTATTTT
GGTAAAGAAGGATTGTCAAAGTGTCCAGTCTATCCTAGAATCAGTCACAAGTGAGTCTAATTTTCATGATTATACCTTAG
TCTCATTGAATGAAGAATTTAATCATGGATGAAGGCTAAATGTGGGTGCCTGAGCTTGGGACAAGGAAGAGGTCTTGATG
TTTTCTTGTGATGTCGATATATATTTCTCAGCTGAATTCCTTAAGAGTTACCAATAAAATGCTGAGCCAGGTAAGAAGGT
GTTTTACCCTGTGGTGTTCAGCCTTTACAATCCTGCCATTGTTTATGCCAACCAGAACGTGCCACCACCTGTAGAGAGTC
AACTGGTTAACAAAAAGGATTCTGACTTTTGGTGAGATTTTGGCTTTAGGTTGACTTATCAATATTGATCAGATTTCCTG
ACTATTGGTGGATTTGACATGAAAGTGAAAGTTTGCGGTAGAGAAGATGTTCATCTTTATAGAAAATACTTACATGGTGA
CCTTATAGTGGTTTGAATTCCAGTTCCTGGTCTTTTCCATCTCTTGCATGAACAGTACTGTGCTGATAAGCAGTACCACA
CGTGTATACAGTCCAAAGTCATGAACAAGGCCTCTCACTCCCACGTGGGGATGCTGGTCTTCAGAGAGGAAATAGAGACG
CATCTTCATAAACAGGCATACAGGACA

Alignment

ORF - retro_tbel_4730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.74 %
• Parental protein coverage: 56.46 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TQYELFFKKADLMEYRHVTLFRPFGPLMKVKSEMIDITRSIINIIVPLAERTEAFAQFMQNFRDVCIHQD
          TQYELFFKKADLM.YR.VT.F..FGPLMK.K.EMIDIT.SIINIIVPLAERT.AFAQFMQNFRDVCI.Q.
Retrocopy TQYELFFKKADLMDYRNVTHFHLFGPLMKIKTEMIDITGSIINIIVPLAERTQAFAQFMQNFRDVCIYQA

Parental  KRIHLTVVYFGKEGLSK-VKSILESVTSESNFHNYTLVSLNEEFNRGRGLNVGARAWDKGEVLMFFCDVD
          KRIHLTVVYFGKEGLSK.V.SILESVTSESNFH.YTLVSLNEEFN.G..LNVGA.AWDK.EVLMF.CDVD
Retrocopy KRIHLTVVYFGKEGLSK>VQSILESVTSESNFHDYTLVSLNEEFNHG*RLNVGA*AWDKEEVLMFSCDVD

Parental  IYFSAEFLNSCRLNAEPGKKVFYPVVFSLYNPAIVYANQDVPPPVEQQLVHKKDSGFWRDFGFGMTCQYR
          IYFSAEFL.S...NAEPGKKVFYPVVFSLYNPAIVYANQ.VPPPVE.QLV.KKDS.FW.DFGF..T.QY.
Retrocopy IYFSAEFLKSYQ*NAEPGKKVFYPVVFSLYNPAIVYANQNVPPPVESQLVNKKDSDFW*DFGFRLTYQY*

Parental  SDFLAIGGFDMEVKGWGGEDVHLYRKYLHGDLIVVRTPVPGLFHLWHEKRCADELTPEQYRMCIQSKAMN
          SDFL.IGGFDM.VK..G.EDVHLYRKYLHGDLIVV..PVPGLFHL.HE..CAD.....QY..CIQSK.MN
Retrocopy SDFLTIGGFDMKVKVCGREDVHLYRKYLHGDLIVV*IPVPGLFHLLHEQYCAD----KQYHTCIQSKVMN

Parental  EASHSHLGMLVFREEIETHLHKQAYRT
          .ASHSH.GMLVFREEIETHLHKQAYRT
Retrocopy KASHSHVGMLVFREEIETHLHKQAYRT

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_4730 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4730 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 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 ,