RetrogeneDB ID: retro_ogar_2142

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873596.1:6884166..6884861(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000011040
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EAF1
• Ensembl ID: ENSOGAG00000013964
• Aliases: None
• Description: ELL associated factor 1 [Source:HGNC Symbol;Acc:20907]

Sequence

>retro_ogar_2142
TTTAAGCCAGCATCTATAGACACTTCATGTGAAGGAGAGCTTCAGGTTGGCAAAGGAGACGAAGTCACAATTATACTGCC
ACACATCCCTGGATCCACACCACCATTGACTATGTTCAAAGGAAACAAACGGCCTTACCAGCAAGACTGTGTACTTATTA
TTAATCATGACATTGGTGAATATGTGCTGGAAAAACTCAGTAGCAGCGTTCAAGTGAAGAAAATAGGAGCTGAAGGAAAC
AGTAAAATCCAGACCCAAATGGAACAACAGCCCACTCGTACCCCACAGCCATCACAGCCACCACCACCTCCACCACCTGT
CCCATTCAGAGCTCCAATGAAGCCTCCAGTTGGACCCAAAACTTCTCCCTTGAAAGATAACCCCTCGCCTGAACCTCAGT
TGGATGACATCAAAAGAGAGCTGAGGGCTGAAGTTGACATTATTGAACAGACGAGCAGCAGCAGTGGGAGCAGCTCCCCG
GATTCTGAGAGCTCTTCGGGAAGTGATGACGACAGCTCCAGCAGTGGAGGGAGGACAATGGCCCAGCCTCTTCTCCACAG
CTTTCACACCAGCAGCCCTCCAACAGCAGGCCTGCCATTGCCAATGGAACCAGCCGGCCACAAGGAAGCAACCCGCTTAT
GAACACCCTCAGAAATGACTTACAGTTAAGCGAGTCTGGCAGTGACAGTGATGAC

Alignment

ORF - retro_ogar_2142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.85 %
• Parental protein coverage: 86.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FKPASIDTSCEGELQVGKGDEVTITLPHIPGSTPPMTVFKGNKRPYQKDCVLIINHDTGEYVLEKLSSSI
          FKPASIDTSCEGELQVGKGDEVTI.LPHIPGSTPP.T.FKGNKRPYQ.DCVLIINHD.GEYVLEKLSSS.
Retrocopy FKPASIDTSCEGELQVGKGDEVTIILPHIPGSTPPLTMFKGNKRPYQQDCVLIINHDIGEYVLEKLSSSV

Parental  QVKKTRAEGSSKIQARMEQQPTRTPQPSQPPPPPPPMPFRAPMKPPVGPKTSPLKDNPSPEPQLDDIKRE
          QVKK..AEG.SKIQ..MEQQPTRTPQPSQPPPPPPP.PFRAPMKPPVGPKTSPLKDNPSPEPQLDDIKRE
Retrocopy QVKKIGAEGNSKIQTQMEQQPTRTPQPSQPPPPPPPVPFRAPMKPPVGPKTSPLKDNPSPEPQLDDIKRE

Parental  LRAEVDIIEQMSSSSGSSSSDSESSSGSDDDSSSSGG-EDNGPASSPQPSHQQPYNSRPAIANGTSRPQG
          LRAEVDIIEQ.SSSSGSSS.DSESSSGSDDDSSSSGG.EDNGPASSPQ.SHQQP.NSRPAIANGTSRPQG
Retrocopy LRAEVDIIEQTSSSSGSSSPDSESSSGSDDDSSSSGG<EDNGPASSPQLSHQQPSNSRPAIANGTSRPQG

Parental  STQLMNTLRNDLQLSESGSDSDD
          S..LMNTLRNDLQLSESGSDSDD
Retrocopy SNPLMNTLRNDLQLSESGSDSDD

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_2142 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
Canis familiaris	ENSCAFG00000006017	1 retrocopy	retro_cfam_1658,
Choloepus hoffmanni	ENSCHOG00000007449	4 retrocopies	retro_chof_1039, retro_chof_2342, retro_chof_355, retro_chof_883,
Erinaceus europaeus	ENSEEUG00000002084	1 retrocopy	retro_eeur_254,
Monodelphis domestica	ENSMODG00000014543	1 retrocopy	retro_mdom_290,
Otolemur garnettii	ENSOGAG00000013964	1 retrocopy	retro_ogar_2142 ,
Sarcophilus harrisii	ENSSHAG00000006597	2 retrocopies	retro_shar_485, retro_shar_56,