RetrogeneDB ID: retro_ogar_1936

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873575.1:10671353..10672305(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000015398
• Aliases: None
• Description: None

Sequence

>retro_ogar_1936
AGACTTGATCTTATTGACATGCAGCTGCAAAAAGTGCTGATGAAGTGGAAAGAGATAGCTGAAAGGTATGATCGCTTGCT
GGGACCAGCTCTATTACCCTTGTGGGTAAATACACCAACTTCTCAGACTTTATGCCTCTGAATTTAAAGCTCTAGAGCAT
TCTTCACTGGCCATCAACCACAAATTAGAAATCAAGTACATAGATTCAACGAACTTGGAGCCAAGCATCTCCCCAGAAGG
GTCTGTGTGCTACCATGAGGCTTGGTAGAACTTCTGTAATGCTTATGGAGTGCTAGTTCCTAGAAGATTTGGTGCTTGAA
GAATGGAAGGGAAAAAACCAGGGAAACACCTGGGTTTGGAAACAGAAAATGCCTTTCATGGATGTGCACTTAGTAATGCA
GTTGGCACTGGTTGAATTCTCAAGAAATATGCTGGGATAGCAAGATGGTAATTCTGCTGAGTTTGACCCTGAGGCTAGTC
ACCCCATGGTAATATACATGCCAGAACATAACCCTGGTTAGGTGAGCAGAACCATAAGGCTGGGCAAGCAGAAAAAACTG
TTCAGACCAACATCTTGATCATGGGGAACCTCTAGGGAGGTACAGACTATCTGGGAGAGAGGCAGCACCACAGATGTGAG
GTAATCCAGCCTTGAAAAACTGTTTGGGAGAGCATGTCTTAAAAGTTTGTTGTCTAAGATGTTGAAGGACAAAGAATGGA
AACTGTGGGGTTGGAAGATCATCCTTTTTTTGTTGGGGTTCAGTAGCACCTTGAGTTCTTGGCCAGATCTATCAAGTCCT
CCCAACCCTACCTTGGTCTCTTTTTGGCCTATGTGGGGTGGCTCTAGAAAGGCTGACAGCTCTTGCCCAGGGACACCTAT
AGTGACAGAAGTGGAAAAAGCTCTCCTGATTCTGAAATTGCTGAATCAAGGTTGCCATCAGTAAATCATGAC

Alignment

ORF - retro_ogar_1936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.96 %
• Parental protein coverage: 54.65 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RLDLPIERQPRKMLMKWKEMADRYDRLLE-TCSIALVGKYTKFSDS-YASVIKALEHSALAINHKLEIKY
          RLDL.I..Q..K.LMKWKE.A.RYDRLL..T.SI.LVGKYT.FSD..YAS..KALEHS.LAINHKLEIKY
Retrocopy RLDL-IDMQLQKVLMKWKEIAERYDRLLG<TSSITLVGKYTNFSDF<YASEFKALEHSSLAINHKLEIKY

Parental  IDSTDLEPSTSQEEPVRYHEAWQKLCSAHGVLVPGGFGVRGTEGKI-QAIAWARKQKKPFLGVCLGMQLA
          IDST.LEPS.S.E..V.YHEAW...C.A.GVLVP..FG....EGK..Q...W..KQK.PF..V.L.MQLA
Retrocopy IDSTNLEPSISPEGSVCYHEAW*NFCNAYGVLVPRRFGA*RMEGKK>QGNTWVWKQKMPFMDVHLVMQLA

Parental  VVEFSRNVLGWQDANSTEFDPKTSHPVVIDMPEHNPGQMGGTMRLGKRRTLF-QTKNSIMRKLYGDPDYL
          .VEFSRN.LG.QD.NS.EFDP..SHP.VI.MPEHNPG....T.RLGK...LF.QT...IM..L.G..DYL
Retrocopy LVEFSRNMLG*QDGNSAEFDPEASHPMVIYMPEHNPG*VSRTIRLGKQKKLF<QTNILIMGNL*GGTDYL

Parental  EERHRHRFEV-NPVLKNCLEEQGL-KFVGQDVEGERMEIVELEDHPFFVGVQYHPEFLSRPIKPSPPYFG
          .ER..HR.EV.NP.LKNCL.E..L.KFV..DVEG.RME.V.LEDHPFFVGVQ.H.EFL.R.IK.S.PY.G
Retrocopy GERQHHRCEV<NPALKNCLGEHVL>KFVV*DVEGQRMETVGLEDHPFFVGVQ*HLEFLARSIKSSQPYLG

Parental  LLLASVGRLPHYLQKGCRLSPRDTYSDRSGSSSPDSEITELKFPSINHD
          L.LA.VG.....L.KG..L.PRDTYSDRSG.SSPDSEI.E...PS.NHD
Retrocopy LFLAYVG----WL*KG*QLLPRDTYSDRSGKSSPDSEIAESRLPSVNHD

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_1936 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
Choloepus hoffmanni	ENSCHOG00000005540	1 retrocopy	retro_chof_2469,
Cavia porcellus	ENSCPOG00000003389	1 retrocopy	retro_cpor_271,
Otolemur garnettii	ENSOGAG00000001255	1 retrocopy	retro_ogar_2926,
Otolemur garnettii	ENSOGAG00000015398	1 retrocopy	retro_ogar_1936 ,