RetrogeneDB ID: retro_tbel_3287

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_135924:56543..56940(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: B4GALT4
• Ensembl ID: ENSTBEG00000012268
• Aliases: None
• Description: UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4 [Source:HGNC Symbol;Acc:927]

Sequence

>retro_tbel_3287
AAACAGAAACACCTTATGTATCTGCTAGAGCATCCTCACCCCTTCCTGCAGAGGCAGCAGCTGGAATATGGCATCTACAT
TATCCACCAGGCTGGAAATAAAAAGTTTAATCAAGCCAAACTCTTGAACGTGGGCTATCTAGAAGCTCTCAAGAAAGAAA
ATTGGGACTGCTTTATATTCCACAACAATGACCTGGTGCCCAGGAATGACTTTAACCTGTACAGGTGTGAAGATCAGCCC
AAGCACCTGGTGGTGGGGAGGTACAGCATCAGTGCAGGTTACACTACAATGGATATTTTGGGGGTGTTACTGCCCTCACA
GAGAACAATTTTTCAAGGTGAATGGATTCTCTAACAACTACTGGGGATGGGGAGGTCAAGACGTGGACCTCAGACTC

Alignment

ORF - retro_tbel_3287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.93 %
• Parental protein coverage: 50.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  REKHLMYLLEHLHPFLQRQQLEYGIYIIHQAGNKKFNRAKLLNVGYLEALKKENWDCFIFHDVDLVPEND
          ..KHLMYLLEH.HPFLQRQQLEYGIYIIHQAGNKKFN.AKLLNVGYLEALKKENWDCFIFH..DLVP.ND
Retrocopy KQKHLMYLLEHPHPFLQRQQLEYGIYIIHQAGNKKFNQAKLLNVGYLEALKKENWDCFIFHNNDLVPRND

Parental  FNLYKCEDQPKHLVVGRNSTG-YRLRYSGYFGGVTALS-REQFFKVNGFSNNYWGWGGEDDDLRL
          FNLY.CEDQPKHLVVGR.S....RL.Y.GYFGGVTAL..REQFFKVNGFSNNYWGWGG.D.DLRL
Retrocopy FNLYRCEDQPKHLVVGRYSIS<CRLHYNGYFGGVTALT<REQFFKVNGFSNNYWGWGGQDVDLRL

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_3287 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3287 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013334	1 retrocopy	retro_ecab_177,
Tupaia belangeri	ENSTBEG00000012268	1 retrocopy	retro_tbel_3287 ,