RetrogeneDB ID: retro_ogar_2087

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873589.1:6398188..6398498(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHD
• Ensembl ID: ENSOGAG00000008568
• Aliases: None
• Description: succinate dehydrogenase complex, subunit D, integral membrane protein [Source:HGNC Symbol;Acc:10683]

Sequence

>retro_ogar_2087
ATGGAGGTTCTCTGAATCCTGAGCATCCTCTGTGGTGCCCAAGGAGGCCAAGCTCTTTTCCTCCGAACCCCTGTGGTCAG
ACCAGCGTGAGTCTCAGCATTTCTCCAGGACTGACCCACCCCAGGGTGGTGTGGAGCAGAGCGCATGCACCTGTCACCAA
TCCGCCATGCTGGTCCTAAGGCTGCATCTCCCCCCTGGACTAGTGAGAGGGTTGTCAGTGTTTTGCTCCTGGGTCTGCTT
CCAGCTTCTTCTTTGAATCCCTTGTTCTGCGATGGACCCCTTGGCTGCAGCCCTTACTCTCCACAGTCAC

Alignment

ORF - retro_ogar_2087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALCRLSVLCGAQGGRVLFLRTSVVRPAYVSAFLQDRPAPGWCGVQHIHLSPSHHSASKAASLHWTSER
          M..L..LS.LCGAQGG..LFLRT.VVRPA.VSAFLQD.P.PGWCG....HLSP..H...KAAS..WTSER
Retrocopy MEVL*ILSILCGAQGGQALFLRTPVVRPA*VSAFLQD*PTPGWCGAERMHLSPIRHAGPKAASPPWTSER

Parental  VVSVLLLGLLPAAYLN-PCSAMDYSLAAALTLHSH
          VVSVLLLGLLPA..LN.PCSAMD..LAAALTLHSH
Retrocopy VVSVLLLGLLPASSLN>PCSAMD-PLAAALTLHSH

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_2087 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 8 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010975	4 retrocopies	retro_cjac_1385, retro_cjac_1390, retro_cjac_1557, retro_cjac_3829,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Otolemur garnettii	ENSOGAG00000008568	5 retrocopies	retro_ogar_1651, retro_ogar_1795, retro_ogar_2087 , retro_ogar_3122, retro_ogar_3147,
Pongo abelii	ENSPPYG00000003876	5 retrocopies	retro_pabe_1549, retro_pabe_1924, retro_pabe_2233, retro_pabe_2999, retro_pabe_3096,