RetrogeneDB ID: retro_ogar_2565

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873634.1:5291118..5291467(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX12
• Ensembl ID: ENSOGAG00000008973
• Aliases: None
• Description: sorting nexin 12 [Source:HGNC Symbol;Acc:14976]

Sequence

>retro_ogar_2565
CGCTTCACCACCCATGAGGTTCCCATGCAGACAAACCTACCTATCTTCAAGCTGAAGGAGTCCTGCGAATGGCGGCGTGA
CAGTGACTTTGAGTGGCTGAAAAACGAGCTGGAGCGAGACAGTAAGAGTGCAGTACCACCACTGCCAGGGAAAGCCTGGA
CGCGGCAGCTCCCTTTCCGAGGAGATGAAGGGATCTTTGAAGAATCTTTCATTGAAGAAAGGAGGCAGGGCCTTGAACAG
TTTATTAACAAAATTGCTGGGCACCCACTGCTCAGAACGAATGCTGCCTGCGCATGGTCCTGCAGGAGGAGGCAATTGAC
GGGAACTATGTCCTGGGAAGGTGCGCCAG

Alignment

ORF - retro_ogar_2565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RFTTYEVRMRTNLPIFKLKESCVRRRYSDFEWLKNELERDSKIVVPPLPGKALKRQLPFRGDEGIFEESF
          RFTT.EV.M.TNLPIFKLKESC..RR.SDFEWLKNELERDSK..VPPLPGKA..RQLPFRGDEGIFEESF
Retrocopy RFTTHEVPMQTNLPIFKLKESCEWRRDSDFEWLKNELERDSKSAVPPLPGKAWTRQLPFRGDEGIFEESF

Parental  IEERRQGLEQFINKIAGHPL-AQNERCLHMFLQEEAIDRNYV-PGKVRQ
          IEERRQGLEQFINKIAGHPL.AQNE.CL.M.LQEEAID.NYV.PGKVRQ
Retrocopy IEERRQGLEQFINKIAGHPL<AQNECCLRMVLQEEAIDGNYV<PGKVRQ

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_2565 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007871	1 retrocopy	retro_btau_1080,
Dasypus novemcinctus	ENSDNOG00000018281	1 retrocopy	retro_dnov_9,
Oryctolagus cuniculus	ENSOCUG00000014919	1 retrocopy	retro_ocun_1286,
Otolemur garnettii	ENSOGAG00000008973	1 retrocopy	retro_ogar_2565 ,
Rattus norvegicus	ENSRNOG00000004036	2 retrocopies	retro_rnor_1751, retro_rnor_501,
Sorex araneus	ENSSARG00000001830	1 retrocopy	retro_sara_452,