RetrogeneDB ID: retro_ogar_1942

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873576.1:9792453..9793142(+)
• Located in intron of: ENSOGAG00000008927

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBP
• Ensembl ID: ENSOGAG00000016187
• Aliases: None
• Description: emopamil binding protein (sterol isomerase) [Source:HGNC Symbol;Acc:3133]

Sequence

>retro_ogar_1942
ATGACCACCAATGCTGGCCCCTTGCATCCATACTGGCCTCAGAACCTAAAGCTGGCTAACTTATACCTAATGAATATTCC
ACCTGGCATCTCCTGGCTGACCTCTTCTCTGTCTGTGGGGTCTTAGTCACGACCACATGGCATTTGTCCAGTTGTGCTGC
TGTTGTTCCACTGGGGACTTGGTGGCGACTGTGCCTGTGCTGCTTTGCAGTGTGTGGATTTATTCACCTGACTATTAAGG
GCTGGGTCATTCTCTACCATGAGGACGTTCTTGGAGACCAAGCCTTCTTATCCCAACTCTGGTAAGAATATGCCAAGGCA
GATAGCCGATACATCCCGGGTGACAAGTTCATGGTATGCATGGAAACCATCACAGTTTTACTGTGGGGACCACTCAGCCT
ATGGGTGGTGATCGCCTTTCTCCACCAGCAACCCTTCCGCTTTGTCCTACAGCTTGTGGTCTTGGTGGGCCAGATCTATG
GGGACATACTGTACTTCCCGACAGAGTACAATGATGGATTCTAGCATGGTGAGCTGGGCCATCCCCTCTACTTCTGGTTT
TACTTTGTCTTCATGAATTCCCTATGGATTATGCTGCCTGGAATCCTTGTGTTTGATTCTGTGAAGCAGCTAACACATGC
CCAGAGTATGCTGGATGTGAAGGTCACAAAAACCAAGAGTAAGAAGAAT

Alignment

ORF - retro_ogar_1942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTNAGPLHPYWPQNLKLDNF-VPNEYSTWHLLAGLFSVCGVLVMTTWHLSSHAAVVPLGTWRRLSLCWF
          MTTNAGPLHPYWPQNLKL.N...PNEYSTWHLLA.LFSVCGVLV.TTWHLSS.AAVVPLGTW.RL.LC.F
Retrocopy MTTNAGPLHPYWPQNLKLANL<IPNEYSTWHLLADLFSVCGVLVTTTWHLSSCAAVVPLGTWWRLCLCCF

Parental  AVCGFIHLAIEGWFILYHEDLLGDQAFLSQLWKEYAKGDSRYILGDNFTVCMETITVLLWGPLSLWVVIA
          AVCGFIHL.I.GW.ILYHED.LGDQAFLSQLW.EYAK.DSRYI.GD.F.VCMETITVLLWGPLSLWVVIA
Retrocopy AVCGFIHLTIKGWVILYHEDVLGDQAFLSQLW*EYAKADSRYIPGDKFMVCMETITVLLWGPLSLWVVIA

Parental  FLHQQPFRFVLQLVVSVGQIYGDIMYFLTEYKDGFQHGELGHPLYFWFYFVFMNSLWIVLPGILVFDSVK
          FLHQQPFRFVLQLVV.VGQIYGDI.YF.TEY.DGF.HGELGHPLYFWFYFVFMNSLWI.LPGILVFDSVK
Retrocopy FLHQQPFRFVLQLVVLVGQIYGDILYFPTEYNDGF*HGELGHPLYFWFYFVFMNSLWIMLPGILVFDSVK

Parental  QLTHAQSMLDMKVTKAKSKKN
          QLTHAQSMLD.KVTK.KSKKN
Retrocopy QLTHAQSMLDVKVTKTKSKKN

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_1942 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009287	1 retrocopy	retro_btau_1337,
Dipodomys ordii	ENSDORG00000013766	1 retrocopy	retro_dord_32,
Otolemur garnettii	ENSOGAG00000016187	3 retrocopies	retro_ogar_1190, retro_ogar_1191, retro_ogar_1942 ,
Procavia capensis	ENSPCAG00000009202	1 retrocopy	retro_pcap_218,