RetrogeneDB ID: retro_ogar_1659

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873559.1:6086222..6086940(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000032550
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM118B
• Ensembl ID: ENSOGAG00000008923
• Aliases: None
• Description: family with sequence similarity 118, member B [Source:HGNC Symbol;Acc:26110]

Sequence

>retro_ogar_1659
ATGGCTTCTACAGGAAGCCAGGACTCTGATATAGATGAGATTTTTGGATTCTTCATTGATGGCACACCCCCACCAAAAAT
CCCAGGAAGCTGCTTCCAAGCTTAAAAACTAAGAAGCCTCAGGAACTCATGCTAGTGATTGGCACAGGCATCAGTGCTGC
CCTTGCCCCTCAGGTTCCAGCCCTGAAATCCTGGAAGGGGTTGATCCATGCCTTGCTGGATGCTGCCATCAATTTTGATC
TTCTAGAAGATGTGGAGAGCAAAAAGTTTCAGAAGTGTCTCCATGAAGTCAAGAACCTTGTCCATGTTGCCCATGACCTT
AATCCAGAAACTCTCCTCGCACCAGTAATGTTTGATCCACATTTTTCAAAGACTGTTTATATGAAGTATTTGACGACTTG
GAGTCAAAGATGGAAGATTCCGGAAAACAGCTACTTCAGTCAGTTCTCCACTTGATGGAAAATGGAGCCCTCATATTAAC
TACAAATTTTGATAATCTCCTGGAAATGTATGGAGCAGACCAGGATATACAACTGGAATCCGCTGACCTTACTGACGAGA
AAAAGGTCCTCAACTGGGCCCAGGAGAAGAGGAAACTGAGTGTGCTGCACATCCATGGGGTCTACACCAACCCTAGCGGC
ATTGTCCTTCATCCAGCAGAATATCAGAATGTGCTCAGGAACACTGAAGTTATGAGAGAGATTCAGAAACTATGAGAA

Alignment

ORF - retro_ogar_1659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.84 %
• Parental protein coverage: 68.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASTGSQASDIDEIFGFFSDGAPP-TKKPRKLLPSLKTKKPRELVLVIGTGISAAVAPQVPALKSWKGLI
          MASTGSQ.SDIDEIFGFF.DG.PP.TK.PRKLLPSLKTKKP.EL.LVIGTGISAA.APQVPALKSWKGLI
Retrocopy MASTGSQDSDIDEIFGFFIDGTPP<TKNPRKLLPSLKTKKPQELMLVIGTGISAALAPQVPALKSWKGLI

Parental  QALLDAAIDFDLLEDEESKKFQKCLHEDKNLVHVAHDLIQKL-SPRTSNVRSTFFKDCLYEVFDDLESKM
          .ALLDAAI.FDLLED.ESKKFQKCLHE.KNLVHVAHDL.....SPRTSNV.STFFKDCLYEVFDDLESKM
Retrocopy HALLDAAINFDLLEDVESKKFQKCLHEVKNLVHVAHDLNPET<SPRTSNV*STFFKDCLYEVFDDLESKM

Parental  EDSGKQLLQSVLHLMENGALVLTTNFDNLLELYAADQGKQLESLDLTDEKKVLEWAQEKRKLSVLHIHGV
          EDSGKQLLQSVLHLMENGAL.LTTNFDNLLE.Y.ADQ..QLES.DLTDEKKVL.WAQEKRKLSVLHIHGV
Retrocopy EDSGKQLLQSVLHLMENGALILTTNFDNLLEMYGADQDIQLESADLTDEKKVLNWAQEKRKLSVLHIHGV

Parental  YTNPSGIVLHPAGYQNVLRNTEVMREIQKLYE
          YTNPSGIVLHPA.YQNVLRNTEVMREIQKL.E
Retrocopy YTNPSGIVLHPAEYQNVLRNTEVMREIQKL*E

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_1659 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016718	1 retrocopy	retro_dord_554,
Erinaceus europaeus	ENSEEUG00000007898	1 retrocopy	retro_eeur_605,
Myotis lucifugus	ENSMLUG00000017329	1 retrocopy	retro_mluc_1535,
Oryctolagus cuniculus	ENSOCUG00000017049	1 retrocopy	retro_ocun_1272,
Otolemur garnettii	ENSOGAG00000008923	1 retrocopy	retro_ogar_1659 ,