RetrogeneDB ID: retro_tbel_2183

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_103822:14874..15252(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF5
• Ensembl ID: ENSTBEG00000016320
• Aliases: None
• Description: ring finger protein 5, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:10068]

Sequence

>retro_tbel_2183
CTGGAGACGTGGCCAGAGCGGCAAGAATGCCCAGTGTGTAAAGCTGGGATCAACAGAGAGAAGGTCGTCCCGCTTTATGG
GCGAGGGAGCCAGAAGCCTCAGGATCCCAGACTGAAGACCCCACCCTGCCCCTAGGGCCAGCGCCCAGCTCCAGAGAGCA
GAGGGGGATTCCAGCCATTTGGTGACACCGGGGGCTTTCACTTCTCATTTGGTGTTGGTGCTTTTCCCTTTGGCTTTTTC
ACCACCATCTTCAATACCCACGAGCCTTTCCGCGGGGCCACAGGTGTGGATCTGGGACAGGGTCACCCAACCTCCAGTTG
GCAGGATTCCTTCTTCCTGTTTCTCACCATTTTCTTCTTTCTTTGACTGCTCAGTATT

Alignment

ORF - retro_tbel_2183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.06 %
• Parental protein coverage: 70.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LETRPERQECPVCKAGISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRGGFQPFGDTGGFHFSF
          LET.PERQECPVCKAGI.REKVVPLYGRGSQKPQDPRLKTPP.P.GQRPAPESRGGFQPFGDTGGFHFSF
Retrocopy LETWPERQECPVCKAGINREKVVPLYGRGSQKPQDPRLKTPPCP*GQRPAPESRGGFQPFGDTGGFHFSF

Parental  GVGAFPFGFFTTVFNTHEPFRRATGVDLGQGHPTSSWQDSLFLFLAIFFFFWLLSI
          GVGAFPFGFFTT.FNTHEPFR.ATGVDLGQGHPTSSWQDS.FLFL.IFFF..LLSI
Retrocopy GVGAFPFGFFTTIFNTHEPFRGATGVDLGQGHPTSSWQDSFFLFLTIFFFL*LLSI

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_2183 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2183 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000016417	1 retrocopy	retro_ocun_1241,
Otolemur garnettii	ENSOGAG00000031466	1 retrocopy	retro_ogar_1951,
Oreochromis niloticus	ENSONIG00000013523	1 retrocopy	retro_onil_48,
Ochotona princeps	ENSOPRG00000004366	2 retrocopies	retro_opri_166, retro_opri_667,
Pan troglodytes	ENSPTRG00000018010	1 retrocopy	retro_ptro_2740,
Ictidomys tridecemlineatus	ENSSTOG00000024478	1 retrocopy	retro_itri_480,
Tupaia belangeri	ENSTBEG00000016320	1 retrocopy	retro_tbel_2183 ,