RetrogeneDB ID: retro_tbel_4300

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_75894:3267..3661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAL2
• Ensembl ID: ENSTBEG00000001716
• Aliases: None
• Description: mal, T-cell differentiation protein 2 (gene/pseudogene) [Source:HGNC Symbol;Acc:13634]

Sequence

>retro_tbel_4300
CTGTTTGGGGTCTCATCTGGATTTTGGTTGCCTCCTCCAATGTTCCTCTACCTCTGCTACAAGGATAGGTCATGTTTGTG
TCGTGAGAGCTGGTTTCTTCTACCTCCTCTTCCTGGGTGTCTTCCTCTCTGGCATGGTGACTCAGATTGATGCCAACTGG
AACTTCTTGGATTTTGCCTATCATTTTACAGTGTTTGTTTTCTACTTTGGAGCCTTCTTATTAGAAGCAGCAGCCACATC
TCTGCACGATCTGCATTGCAATACAACCGCATCTGTGCAGCCACTCCTGAGTGACAACCAGTATAACATCAACGTAGCAG
CCACAATTTTTGCCTTTGTGACAACAGTTTGTTTTGTTTGCAGTTTGGGTCTGGCTTTATGAAGATGGTGACCG

Alignment

ORF - retro_tbel_4300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFG-GLVWILVASSNVPLPLLQGWVMFVS-VTAFFFSLLFLGVFLSGTVTQIDANWNFLDFAYHFTVFVF
          LFG.GL.WILVASSNVPLPLLQG.VMFVS.V.A.FF.LLFLGVFLSG.VTQIDANWNFLDFAYHFTVFVF
Retrocopy LFG<GLIWILVASSNVPLPLLQG*VMFVS<VRAGFFYLLFLGVFLSGMVTQIDANWNFLDFAYHFTVFVF

Parental  YFGAFLLEAAATSLHDLHCNTTTSVQPLLSDNQYNINVAATIFAFVTTVCYGCSLGLALRRWRP
          YFGAFLLEAAATSLHDLHCNTT.SVQPLLSDNQYNINVAATIFAFVTTVC..CSLGLAL.RW.P
Retrocopy YFGAFLLEAAATSLHDLHCNTTASVQPLLSDNQYNINVAATIFAFVTTVCFVCSLGLAL*RW*P

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_4300 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4300 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000001514	2 retrocopies	retro_sara_229, retro_sara_553,
Tupaia belangeri	ENSTBEG00000001716	1 retrocopy	retro_tbel_4300 ,