RetrogeneDB ID: retro_ogar_3397

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873817.1:780956..782135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIMKLA
• Ensembl ID: ENSOGAG00000000458
• Aliases: None
• Description: ribosomal modification protein rimK-like family member A [Source:HGNC Symbol;Acc:28725]

Sequence

>retro_ogar_3397
ATGTGCTCCCAGCTCTGGTTCCTGACCGACTGGCGCATCCAGGAGGACTACCCTCAGGTGCAGATCCTACAGCCCCTCCG
GCAGTGCTGCTCTGAGAATCACGTGTGCTTCCGGGTGGTGCTCTGGGACCAGATCACAGTCACCATTGTTGGCGGCCACC
TCTGCCTCCAGCTGAACCAGAAGACCCTCACCACCTTCCTGGATGTGGTGCTTGTGCGAGTGCCCACACCATCAGCGCAG
TTGGATAGTGACATTACTGTCCTGCAACATCTGGAGAAGCTGGGCTGCTGCTTGGTCAACCGCCTGCAAAGCATCTTAAA
TTGCATCAACAAATTTTGTACATTCCAAGAGCTGGCTGGATGAGAGGTCCCAATGCCAGACACCTTCTCCTATGGTAGAC
ATGAAGACTTCTCAATATTGATTTATGAAGCTGAGCCCTTGGGCTACCCAGTTGTGGTGAAGAGCACCAGAGGCCACTGG
GGGAAAGCTGTTTTTCTAGCAAGAGATAAACATCACCTCTCAGACATCTGCCATCTGATCCGCCATGAGGTGCCCTACAT
ATTCCAGAAGTATGTGAAGGAGTCGCATGGAAAGGACATCGGTGTAGTGGTGGTAGTGGGCCAGGTGATAGTCTCATTGC
TTCTCTTCTCCACAGATGGACAGATGCAAAGCAACCGCTCTCTAAGTAGTGTGGGCATCATGTGCTCGCTGAAAGAACAA
GGCAAGCAGTTGGCTATACAGGTGTCCAACATCCTGGGCATGGAATTCTGTGGCATTGACCTCCTTATCATGGATGATGG
CTCCTTTGTGGTGTGTGAGGCAAATGCCAATGTTGGCTTCCTAGCCTTCTACCAGGCATGCAACTTAGATGTGGGTGGGA
TCATTGCAGACTATACCATGTCCTTACTGCCAAACAGACACACTGGGAAGGAAGATGGCTGTCTTCCAAGGGATGTCAAG
TCTCTGGGAGAAGAATGAGCCAAGATGTCTGCACTTCAACTCAGGGAGTTGCAGAGAACATCTACACCATCAACAGTGGG
TCTACCTCTAGTGAGAGTGAGCCAGAACTAGGAGAGATCTGGGATTCCTCAGCAAGCACAATGGGGACCCCTCCCCCCCA
TGCTACCCGAGCCTGGCTACAACATTAACAACAGGATTGCTTCAGAATTAAAACTTAAA

Alignment

ORF - retro_ogar_3397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MCSQLWFLTDRRIREDYPQVQILRALRQRCSEQDVSFRAVLMDQIAVTIVGGHLGLQLNQKALTTFPDVV
          MCSQLWFLTD.RI.EDYPQVQIL..LRQ.CSE..V.FR.VL.DQI.VTIVGGHL.LQLNQK.LTTF.DVV
Retrocopy MCSQLWFLTDWRIQEDYPQVQILQPLRQCCSENHVCFRVVLWDQITVTIVGGHLCLQLNQKTLTTFLDVV

Parental  LVRVPTPSVQSDSDITVLRHLEKLGCRLVNRPQSILNCINKFWTFQELAGHGVPMPDTFSYGGHEDFSKM
          LVRVPTPS.Q.DSDITVL.HLEKLGC.LVNR.QSILNCINKF.TFQELAG..VPMPDTFSYG.HEDFS..
Retrocopy LVRVPTPSAQLDSDITVLQHLEKLGCCLVNRLQSILNCINKFCTFQELAG*EVPMPDTFSYGRHEDFSIL

Parental  IDEAEPLGYPVVVKSTRGHRGKAVFLARDKHHLSDICHLIRHDVPYLFQKYVKESHGKDIRVVVVGGQVI
          I.EAEPLGYPVVVKSTRGH.GKAVFLARDKHHLSDICHLIRH.VPY.FQKYVKESHGKDI.VVVV.GQVI
Retrocopy IYEAEPLGYPVVVKSTRGHWGKAVFLARDKHHLSDICHLIRHEVPYIFQKYVKESHGKDIGVVVVVGQVI

Parental  GSMLRCSTDGRMQSNCSLGGVGVMCPLTEQGKQLAIQVSNILGMDFCGIDLLIMDDGSFVVCEANANVGF
          .S.L..STDG.MQSN.SL..VG.MC.L.EQGKQLAIQVSNILGM.FCGIDLLIMDDGSFVVCEANANVGF
Retrocopy VSLLLFSTDGQMQSNRSLSSVGIMCSLKEQGKQLAIQVSNILGMEFCGIDLLIMDDGSFVVCEANANVGF

Parental  LAFDQACNLDVGGIIADYTMSLLPNRQTGKM-AVLP-GLSSPREKNEP-DGCASTQGVAENVYTINNGST
          LAF.QACNLDVGGIIADYTMSLLPNR.TGK....LP.G.SS..EKNEP.D.C.STQGVAEN.YTIN.GST
Retrocopy LAFYQACNLDVGGIIADYTMSLLPNRHTGKEDGCLP>GMSSLWEKNEP>DVCTSTQGVAENIYTINSGST

Parental  SSESEPELGEIRDSSASTMGTP-PPMLPEPGYNINNRIASELKLK
          SSESEPELGEI.DSSASTMGTP.PPMLPEPGYNINNRIASELKLK
Retrocopy SSESEPELGEIWDSSASTMGTP>PPMLPEPGYNINNRIASELKLK

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_3397 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000000458	1 retrocopy	retro_ogar_3397 ,
Otolemur garnettii	ENSOGAG00000011440	2 retrocopies	retro_ogar_1183, retro_ogar_2985,