RetrogeneDB ID: retro_ogar_2973

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873691.1:2983703..2984329(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000027648
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB18
• Ensembl ID: ENSOGAG00000028015
• Aliases: None
• Description: RAB18, member RAS oncogene family [Source:HGNC Symbol;Acc:14244]

Sequence

>retro_ogar_2973
ATGGACGAGGAAGGGCTGACCACTCTAAAGATTCTCTCATCTGCGAGAGTAGGGTGGGCAAATCCAGCCTGCTCTTGAGG
TTCACAGATGATACTTTCGATCCAGAACTTGCAACAACAATAGGTGTTGACTTTAAGGTGAAAACAGTTTCAGTGGATGG
AAATAAGGCTAAATTTGCAATATGGGATACTGCTGGTCAAGAGAGGTTTAGACCATTAACTCCAAGCTATTACAGAGGTG
CACAGGGTGTTATATTAGTTTACGATGTCACAAGAAGGGACACCTTTGTTAAACTGGATAATTGGTTAAATGAATTGGAA
ACATACTGTACAAGAAATGACATAGTAAACATGCTAGTTGGAAATAAAATTGATAAGGAAAATCGTGAAGTCGATAGAAA
TGAAGGCCTGAAGTTTGCAGGAAAGCATTCCATGTTATTTATAGAGGCAAGTGCAAAAACGTGTGATGCACTCAATGTTC
CTCAATGTACCTTTGAGGAACTTGTTGAAAAGATCATTCAGACGCCAGAACTATGGGAAAGTGAGATCCAGAATAAAGGA
GTCAAACTATCACATGGTGAAGAAGGTAGTGGAGGCGGGGCCTGTGGTGGTTATTGTTCTGTGTTA

Alignment

ORF - retro_ogar_2973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDEDVLTTLKIL-IIGESGVGKSSLLLRFTDDTFDPELAATIGVDFKVKTISVDGNKAKLAIWDTAGQER
          MDE..LTTLKIL..I.ES.VGKSSLLLRFTDDTFDPELA.TIGVDFKVKT.SVDGNKAK.AIWDTAGQER
Retrocopy MDEEGLTTLKIL<LICESRVGKSSLLLRFTDDTFDPELATTIGVDFKVKTVSVDGNKAKFAIWDTAGQER

Parental  FRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENREVDRNEGLKF
          FR.LTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENREVDRNEGLKF
Retrocopy FRPLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENREVDRNEGLKF

Parental  ARKHSMLFIEASAKTCDGV---QCAFEELVEKIIQTPGLWESENQNKGVKLSHSEEGSGGGACGGYCSVL
          A.KHSMLFIEASAKTCD.....QC.FEELVEKIIQTP.LWESE.QNKGVKLSH.EEGSGGGACGGYCSVL
Retrocopy AGKHSMLFIEASAKTCDALNVPQCTFEELVEKIIQTPELWESEIQNKGVKLSHGEEGSGGGACGGYCSVL

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_2973 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009871	1 retrocopy	retro_btau_1691,
Choloepus hoffmanni	ENSCHOG00000005565	4 retrocopies	retro_chof_2391, retro_chof_256, retro_chof_396, retro_chof_846,
Cavia porcellus	ENSCPOG00000002234	2 retrocopies	retro_cpor_633, retro_cpor_652,
Dipodomys ordii	ENSDORG00000014338	1 retrocopy	retro_dord_419,
Monodelphis domestica	ENSMODG00000008253	1 retrocopy	retro_mdom_146,
Oryctolagus cuniculus	ENSOCUG00000022307	2 retrocopies	retro_ocun_1699, retro_ocun_841,
Otolemur garnettii	ENSOGAG00000028015	2 retrocopies	retro_ogar_2587, retro_ogar_2973 ,
Rattus norvegicus	ENSRNOG00000018972	2 retrocopies	retro_rnor_2744, retro_rnor_2962,
Sarcophilus harrisii	ENSSHAG00000007613	1 retrocopy	retro_shar_281,