RetrogeneDB ID: retro_ogar_680

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873525.1:12647905..12648523(-)
• Located in intron of: ENSOGAG00000011871

Retrocopy information

• Ensembl ID: ENSOGAG00000027051
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000001521
• Aliases: None
• Description: None

Sequence

>retro_ogar_680
ATGCCTCCCAAGAAGGATGTTCCAGTGAAGAAACCCGCAGGGCCCCCCATCTCCAAACCTACTGCCAAGCCAGCAGCAGG
GGCCCCTCCAGTCAAGACTAAGGCTGAGCCAGCTATTCCCCAAGCTTCTCAGAAAACCCAGGATCCCCTTATTGATCTCT
CCAAAGTTGTGATCGAGTTTAACAAGGACCAGCTGGAGGAGTTCAAAGAAGCATTTGAGCTGTTTGACCGAGTAGGAGAT
GGCAAGATCCTGTACAGCCAGTGTGAGGATGTGATGAGGGCCCTAGGCCAGAACCCCCAACGCCGAGGTGCTCAAGGTCC
TAGGGAACCCCCACAGTGACAAACTGAAGTCCCGGCATGTGGACTTTGAGACTTTCCTGCCTATGCTCCTGGCAGTGGCC
AAGAACCGGGACCAAGGCACATATGAAGACTACTTGGAGGGGCTTCGTGTGTTTGACAAGCAGGGGAATGGCAAAGTCAT
GGGAGCAGAACTCAGACATGTCCTCACCACCCTGGGGGAGAAGATGACTTAGGGGAGGTGGAGACTGTTCTGGCAGGACA
TGAGGACAGCAATGGTTGCATCAACTATGAGGCCTTCCTGAAACACATCCTAAGCGTC

Alignment

ORF - retro_ogar_680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPPKKDVPVKKPAGPPISKPTAKPAAGAPPVKTKAEPAVPQASQKTQDPPIDLSKVVIEFNKDQLEEFKE
          MPPKKDVPVKKPAGPPISKPTAKPAAGAPPVKTKAEPA.PQASQKTQDP.IDLSKVVIEFNKDQLEEFKE
Retrocopy MPPKKDVPVKKPAGPPISKPTAKPAAGAPPVKTKAEPAIPQASQKTQDPLIDLSKVVIEFNKDQLEEFKE

Parental  AFELFDRVGDGKILYSQCGDVMRALG-QNPTNAEVLKVLGNPKSDELKSRRVDFETFLPMLQAVAKNRDQ
          AFELFDRVGDGKILYSQC.DVMRALG...P.NAEVLKVLGNP.SD.LKSR.VDFETFLPML.AVAKNRDQ
Retrocopy AFELFDRVGDGKILYSQCEDVMRALG>RTP-NAEVLKVLGNPHSDKLKSRHVDFETFLPMLLAVAKNRDQ

Parental  GTYEDYLEGLRVFDKEGNGKVMGAELRHVLTTLGEKMT-EEEVETVLAGHEDSNGCINYEAFLKHILSV
          GTYEDYLEGLRVFDK.GNGKVMGAELRHVLTTLGEKMT...EVETVLAGHEDSNGCINYEAFLKHILSV
Retrocopy GTYEDYLEGLRVFDKQGNGKVMGAELRHVLTTLGEKMT<LGEVETVLAGHEDSNGCINYEAFLKHILSV

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_680 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000110	1 retrocopy	retro_cfam_1894,
Callithrix jacchus	ENSCJAG00000011620	3 retrocopies	retro_cjac_113, retro_cjac_2566, retro_cjac_2848,
Dasypus novemcinctus	ENSDNOG00000007592	1 retrocopy	retro_dnov_2073,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Gorilla gorilla	ENSGGOG00000003277	2 retrocopies	retro_ggor_1808, retro_ggor_2233,
Loxodonta africana	ENSLAFG00000012658	1 retrocopy	retro_lafr_734,
Macaca mulatta	ENSMMUG00000005214	1 retrocopy	retro_mmul_962,
Nomascus leucogenys	ENSNLEG00000026948	1 retrocopy	retro_nleu_369,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Otolemur garnettii	ENSOGAG00000001521	3 retrocopies	retro_ogar_1918, retro_ogar_3179, retro_ogar_680 ,
Otolemur garnettii	ENSOGAG00000034596	1 retrocopy	retro_ogar_2549,
Procavia capensis	ENSPCAG00000005927	2 retrocopies	retro_pcap_223, retro_pcap_242,
Pongo abelii	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
Rattus norvegicus	ENSRNOG00000028837	2 retrocopies	retro_rnor_1432, retro_rnor_216,