RetrogeneDB ID: retro_ogar_2033

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873582.1:7519905..7520568(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000034081
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB27A
• Ensembl ID: ENSOGAG00000010405
• Aliases: None
• Description: RAB27A, member RAS oncogene family [Source:HGNC Symbol;Acc:9766]

Sequence

>retro_ogar_2033
ATGTCTGATGGAGATTATGATTACCTCATCAAGTTTTTAGCTTTGGGAGACTCAGGAGTAGGGAAGACCAGTGTACTTTA
TCAGTACACAGATGGTAAATTTAATTCTAAATTTATGACGATGGTGGGGATTGATTTCAGGGAAAAGAGAGTGGTGTACA
GAGCCGATGGGCTGGAAGGAGCCATTGGCAGAGGCCAGAGAATCCACCTGCAGTTATGGGACAGGGCAGTTCAGGAGAGG
TTTCGTAGCTTGGCAACGGCATTCTTCAGAGGTGCTATGGGTTTTCTTCTGCTTTTTGATCTGACAAATGAACAAAGTTT
CCTCAACGTCAGAAACTGGATAACTCAGCTACAAACGCATGCATATTGTGAAAAGCCAGATATAGTGTTATGTGGAAATA
AGGGTGACCTTGAAGACCAGAGAGTAGTAAAAAAGGAAGAAGCCAGGGGACTTGCAGAGAAATACGGAATCCCCTATTTT
GAAACTAGCGTGGCCAATGGGACAAACATAAGCCAAGCAATTGAAATGCTTCTGGGCCTGATCATGAAGCTAATGGAACG
GTGTGTGGACAAGTCCTGGATTCCTGAAGGAGTGGTGCGGTCCAGTGGTCACACCTCTACCAATCAGTTAAGTGAAAACA
AGGAGAAGGGGGTATGTGGCTGT

Alignment

ORF - retro_ogar_2033 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDGDYDYLIKFLALGDSGVGKTSVLYQYTDGKFNSKFITTVGIDFREKRVVYRANGPDGAIGRGQRIHL
          MSDGDYDYLIKFLALGDSGVGKTSVLYQYTDGKFNSKF.T.VGIDFREKRVVYRA.G..GAIGRGQRIHL
Retrocopy MSDGDYDYLIKFLALGDSGVGKTSVLYQYTDGKFNSKFMTMVGIDFREKRVVYRADGLEGAIGRGQRIHL

Parental  QLWDTAGQERFRSLTTAFFRDAMGFLLLFDLTNEQSFLNVRNWISQLQTHAYCENPDIVLCGNKSDLEDQ
          QLWD.A.QERFRSL.TAFFR.AMGFLLLFDLTNEQSFLNVRNWI.QLQTHAYCE.PDIVLCGNK.DLEDQ
Retrocopy QLWDRAVQERFRSLATAFFRGAMGFLLLFDLTNEQSFLNVRNWITQLQTHAYCEKPDIVLCGNKGDLEDQ

Parental  RVVKEEEARGLAEKYGIPYFETSAANGTNISQAIEMLLDLIMKRMERCVDKSWIPEGVVRSNGHTSTSQL
          RVVK.EEARGLAEKYGIPYFETS.ANGTNISQAIEMLL.LIMK.MERCVDKSWIPEGVVRS.GHTST.QL
Retrocopy RVVKKEEARGLAEKYGIPYFETSVANGTNISQAIEMLLGLIMKLMERCVDKSWIPEGVVRSSGHTSTNQL

Parental  SENKEKGVCGC
          SENKEKGVCGC
Retrocopy SENKEKGVCGC

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_2033 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
Bos taurus	ENSBTAG00000012408	1 retrocopy	retro_btau_83,
Otolemur garnettii	ENSOGAG00000010405	1 retrocopy	retro_ogar_2033 ,
Otolemur garnettii	ENSOGAG00000013894	1 retrocopy	retro_ogar_2356,
Otolemur garnettii	ENSOGAG00000016969	1 retrocopy	retro_ogar_2441,