RetrogeneDB ID: retro_tbel_4668

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_97404:43027..43462(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSTBEG00000007092
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]

Sequence

>retro_tbel_4668
CCAAAGGCCAAAAATAAAATTTTTGGCCAATTTAACTAGTACTTCTAGGAGAGTCTGCTGTTGGCAAATCAAGCCTAATG
ATTCATTTTTTGAAAGGCCAATTTCATGAATTTCAGGAGACTACAATTAGGGCTGCTTTTCTAACCCAAACTGTGTGTCT
TGACACAGGAGTAAGTTTGCAATATGAGATACAATTGGCCAGGAGAGATACCGTAGCTTAGCACCGATGTACTACAGAGG
AGCACAAGCAGCCATAGTTGTATATGATATCACAAATGAGGAGCCCATTGCAAGTGCAAAAAAAAACTGGGCTAAAGCAT
TTCAGAAGCAAGCAAGTCCTAATATTGTAATAGCTTTGTCAGGAAACAAGGCTGACCTAGCAATAAAAGAGCTGTAAATT
TCTAGGAAGCACAGTCTTATGCAGATGACAACAGT

Alignment

ORF - retro_tbel_4668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.67 %
• Parental protein coverage: 67.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PAAGNKIC-QFK-LVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFE-IWDTAG
          P.A.NKI..QF..LVLLGESAVGKSSL...F.KGQFHE.QE.TI.AAFLTQTVCL.DT.V....I.DT.G
Retrocopy PKAKNKIFGQFN<LVLLGESAVGKSSLMIHFLKGQFHEFQETTIRAAFLTQTVCL-DTGVSLQ<I*DTIG

Parental  QERYHSLAPMYYRGAQAAIVVYDITNTDTFA-RAKNWVKELQRQASPNIVIALAGNKADLA-SKRAVEFQ
          QERY.SLAPMYYRGAQAAIVVYDITN....A.....W.K..Q.QASPNIVIAL.GNKADLA..KRAV.F.
Retrocopy QERYRSLAPMYYRGAQAAIVVYDITNEEPIASXXXXWAKAFQKQASPNIVIALSGNKADLA<NKRAVNF*

Parental  EAQAYADDNS
          EAQ.YADDNS
Retrocopy EAQSYADDNS

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_4668 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4668 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Gorilla gorilla	ENSGGOG00000005472	1 retrocopy	retro_ggor_2182,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Macaca mulatta	ENSMMUG00000014761	1 retrocopy	retro_mmul_2022,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237,
Tupaia belangeri	ENSTBEG00000007092	1 retrocopy	retro_tbel_4668 ,