RetrogeneDB ID: retro_ogar_2470

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873625.1:2105138..2105656(-)
• Located in intron of: ENSOGAG00000012643

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S5
• Ensembl ID: ENSOGAG00000030827
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 5, muted [Source:HGNC Symbol;Acc:18561]

Sequence

>retro_ogar_2470
ACTGCCACGGGCGGTGGCAACAAGAGGGACAACTGGGGACCGCGGGCACAGCACACCTCATTATCAAGGATCTTGGAGAA
ATTTATTCAAGGCTCTTGGATCACAGACCAGTTATTCAAGGTGATACACATTATTCTATAGAAGAATTTGAAGAAAAACA
TGGTCTTCGAGAAATGCAAGTTCTTGAAAATTTGAAGAATATGGTCCATGAAACAAACGAACATACTCTTCCCAAATGTA
GAGAAACAATGCAGGACGACTTAAGCCAAGTTCTTCAGAGATTGCAAGCAGCTAATGATTCAGTCTATAGACTCCAACAG
AGGGAGCAGGAACGAAAAAAGATTCATAATGACCATTTAATAGCTAGTGAGAAACAGCATTTACTCCAGTGGTAAGACTT
CAGGAAGAAACAGCCCAGCAAAAGGGCTGAAGTGGATGAAGAACACAGAAAAGCCGTGGAGAAGCTCAAAGAACAGTACA
CTGAGATGGAGAAAGACCTAGCAAAATTTTCAGTCTTT

Alignment

ORF - retro_ogar_2470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 93.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TAVGGGNKKRDS-LGTAGTAHLIIKDLGEIHSRLLDHRPVIQGETRYFIKEFEEKRGLREMRVLENLKNM
          TA.GGGNK.RD..LGTAGTAHLIIKDLGEI.SRLLDHRPVIQG.T.Y.I.EFEEK.GLREM.VLENLKNM
Retrocopy TATGGGNK-RDN<LGTAGTAHLIIKDLGEIYSRLLDHRPVIQGDTHYSIEEFEEKHGLREMQVLENLKNM

Parental  VHETNEHTLPKCRETMQDNLSQVLQRLQAANDSVCRLQQREQERKKIHNDHLIASEKQHVLQWEDFMKKQ
          VHETNEHTLPKCRETMQD.LSQVLQRLQAANDSV.RLQQREQERKKIHNDHLIASEKQH.LQW.DF.KKQ
Retrocopy VHETNEHTLPKCRETMQDDLSQVLQRLQAANDSVYRLQQREQERKKIHNDHLIASEKQHLLQW*DFRKKQ

Parental  PSKRAEVDEEHRKAVEKLKEQYAEMEKDLAKFSVF
          PSKRAEVDEEHRKAVEKLKEQY.EMEKDLAKFSVF
Retrocopy PSKRAEVDEEHRKAVEKLKEQYTEMEKDLAKFSVF

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_2470 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017324	1 retrocopy	retro_amel_1747,
Bos taurus	ENSBTAG00000039732	2 retrocopies	retro_btau_1699, retro_btau_1747,
Monodelphis domestica	ENSMODG00000010026	1 retrocopy	retro_mdom_1483,
Oryctolagus cuniculus	ENSOCUG00000025755	2 retrocopies	retro_ocun_1051, retro_ocun_269,
Otolemur garnettii	ENSOGAG00000030827	1 retrocopy	retro_ogar_2470 ,
Ictidomys tridecemlineatus	ENSSTOG00000027342	3 retrocopies	retro_itri_1038, retro_itri_179, retro_itri_1901,