RetrogeneDB ID: retro_ogar_2307

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873610.1:5963391..5963942(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VHL
• Ensembl ID: ENSOGAG00000007587
• Aliases: None
• Description: von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:12687]

Sequence

>retro_ogar_2307
GGCCATGAAGAGTTGGGGGCTGAGGAGTCCAGCCCAGAAGAGTCTGACTGAGAGAAGTTGGATGCCAAGGAGTTGATCCA
TTGCTGGGCAGCTGTGGCCAGCCCTACCCTCAGTAAATTCATGCAAACCCTCCCAAAGTCATTTGCAATTTCAGCCCATG
TGTCGTGCTGCCTGCATGGTTCAACTTCAACAGCCAGCGACAGCCCTATCTGAGGTTGCAGCCCAGCACGGGCCATCCAC
AGCTACCAAGGTCACCTTTTGCTCCTAAGAGATGCAGGAACATATGATAGGCTTCTGGTTAAACAACTGTATTATTTGTG
CCATCTCTCAATGTTGATGGACAGCCTATTTTTGTGAACATCACACTGCCAGTGTATACCCTAAAAGAGTGATGTCTCCA
TGTTGTACAAAGCCTAGTCAAGCCTGAGAATTACAGGAGACTGGACACCTTCAGATCACTCTATGAAGATCTGGAAGACC
ACCTAAATGTATTGAAGGTCCTGGAGCAGCTGACGCAGGAGCATATTGAAAGTCAACAACAAAAAAAAGAG

Alignment

ORF - retro_ogar_2307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.62 %
• Parental protein coverage: 85.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GHEESGAEESGPEESDPEESGTEEEMD-AGRPRPVLRSVNS-REPSQVIFCNRSPRVVLPVWLNFDGEPQ
          GHEE.GAEES.PEESD.E.....E....AG...P.L.SVNS...P..VI.CN.SP.VVLP.W..F....Q
Retrocopy GHEELGAEESSPEESD*EKLDAKELIH>AGQLWPALPSVNS>ANPPKVI-CNFSPCVVLPAW--FNFNSQ

Parental  PYPTLQP-GTGRRIHSYRGHLWLFRDAGTYDGLLVNQ-TELFVPSLNVDGQPIFANITLPVTVYTLKERC
          ..P.L......R.IHSY.GHL.L.RDAGTYD.LLV.Q.T.LFVPSLNVDGQPIF.NITLPV..YTLKE.C
Retrocopy RQPYLRL>SPARAIHSYQGHLLLLRDAGTYDRLLVKQ<TVLFVPSLNVDGQPIFVNITLPV--YTLKE*C

Parental  LQVVRSLVRPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQEHIESQRMGKE
          L.VV.SLV.PENYRRLD..RSLYEDLEDH.NV.K.LE.LTQEHIESQ....E
Retrocopy LHVVQSLVKPENYRRLDTFRSLYEDLEDHLNVLKVLEQLTQEHIESQQXXXE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2307 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000010456	1 retrocopy	retro_ggor_1259,
Otolemur garnettii	ENSOGAG00000007587	1 retrocopy	retro_ogar_2307 ,
Pongo abelii	ENSPPYG00000013663	1 retrocopy	retro_pabe_275,
Ictidomys tridecemlineatus	ENSSTOG00000013959	1 retrocopy	retro_itri_1624,