RetrogeneDB ID: retro_ogar_3444

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873843.1:400753..402089(-)
• Located in intron of: ENSOGAG00000007772

Retrocopy information

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

Parental gene information

• Parental gene symbol: PWP1
• Ensembl ID: ENSOGAG00000011940
• Aliases: None
• Description: PWP1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:17015]

Sequence

>retro_ogar_3444
ATGAACCACAGCCGCCAGGTGATGTGCGTGGCTTGGGTCCACTGCGGCATGGCCAAAGAGACACCAGATAAGGTAGAACT
AAGTAAAGAAGAAGTAAAGTGACTCATTGCTGATGCAAAGGAAAAATTGCAAGAAGAAGGTGGCAGTGATGAAGAGGAGG
TAGGCCATCCTTCAGAAGATGGCATGCAGAGTGCACGTACCCAGGCTCGACCAAGAGAGCCCTTGGAGGATGGTGACCCA
GAGGATGACAGGACGCTAGATGACCATGAGCTGGCCGAGTATGACTTGGATAAATATGATGAAGAGGATGATCCAGATGC
TGAGACTCTTGGCGAATCTCTCTTGGGTCTTACGGTATACAGGAGTAATGATCAAGATCCTTACATTACCTGAAAGATAC
AGAACAATATGAACGTGAAGATTTCTTTAAGCCCAGTGACAATCTTATAGTTTGTGGCCAAGCTGACCAGGACCAGTGCA
ATTTAGAGGGGCACGTTTATAAACAAGAAGAAGACTCTTTTTATGTACACCATGATATACTCTTGTCTGCATATCCTCTG
AGTGTGGAATGGCTGAATTTTGATCCTAACCCAGATGATTCTACTGGAAATTATATTGCTGTGGGAAGCATAACACCTGT
TATTGAAGCATGGGACCTCGATATAGTGGACTCTTTAGAACCCGTCTTCACACTTGGAAGTAAACTTTCAAAAAAGAAGA
AAAAGAAAGGGAAGGAGAGTTCCTCAGCAGAAGGGCATACTGATGCTGTCCTTGACCTTTCATGGAATAAGCTAATGAGA
AATGTATTGGCAAGTGCATCAGCTGATAATACTGTCATTCTGTGGGATATGTCCCTGGGGAAGCCAGCAGCTAGCCTTGC
TGTACACACAGATGAGGTCCAGAATTTGCAGTTTCATCCATTTGAAGCACAAACTCTGATTTCTGGATCTTATGATAAAT
CTGTTGCTTTGTATGACTGCGGAAGCCCAGAAGAAAGCCGTCACATGTGGCGGTTCAGTGGGCAGATCGAGAGGGTGACT
TGGAATCACTTTTCATTTTTTCACTTTTGGCCAGTACAGATGATGGCTTTGTGTATAATTTGGATGCATGTTCAGATAAG
CCAATTTTTACTCTTAATGCCCACAATGATGAAATCTCTTGTCTTGATCTAAGCAGTCAGATCAAGGGTTGTCTTGTGAT
TGCTTCAGCTGACAAATATGTGAAGATCTGGGATATCTTAGATGATAGGCCAAGTCTAGTTCATTCTAGGGGCATGAAAA
TGGGAGTTCTCTTCTGTTCTTCATGTTGCCCTGATTTGCCATTTATTTGCCTATTT

Alignment

ORF - retro_ogar_3444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.98 %
• Parental protein coverage: 89.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNRSRQVTCVAWVRCGVAKETPDKVELSKEEVKRLIADAKEKLQEDGGSDEEEVGHPSEDGMQSARTQAR
          MN.SRQV.CVAWV.CG.AKETPDKVELSKEEVK.LIADAKEKLQE.GGSDEEEVGHPSEDGMQSARTQAR
Retrocopy MNHSRQVMCVAWVHCGMAKETPDKVELSKEEVK*LIADAKEKLQEEGGSDEEEVGHPSEDGMQSARTQAR

Parental  PREPLEDGDPEDDRTLDDDELAEYDLDKYDEEDDPDAETLGESLLGLTVYGSNDQDPYVT-LKDTEQYER
          PREPLEDGDPEDDRTLDD.ELAEYDLDKYDEEDDPDAETLGESLLGLTVY.SNDQDPY.T.LKDTEQYER
Retrocopy PREPLEDGDPEDDRTLDDHELAEYDLDKYDEEDDPDAETLGESLLGLTVYRSNDQDPYIT<LKDTEQYER

Parental  EDFLIKPTDNLIVCGRAEQDQCNLEVHVYNQEEDSFYVHHDILLSAYPLSVEWLNFDPSPDDSTGNYIAV
          EDF..KP.DNLIVCG.A.QDQCNLE.HVY.QEEDSFYVHHDILLSAYPLSVEWLNFDP.PDDSTGNYIAV
Retrocopy EDFF-KPSDNLIVCGQADQDQCNLEGHVYKQEEDSFYVHHDILLSAYPLSVEWLNFDPNPDDSTGNYIAV

Parental  GSMTPVIEVWDLDIVDSLEPVFTLGSKLSKKKKKKGKKSSSAEGHTDAVLDLSWNKLIRNVLASASADNT
          GS.TPVIE.WDLDIVDSLEPVFTLGSKL........K.SSSAEGHTDAVLDLSWNKL.RNVLASASADNT
Retrocopy GSITPVIEAWDLDIVDSLEPVFTLGSKLXXXXXXXXKESSSAEGHTDAVLDLSWNKLMRNVLASASADNT

Parental  VILWDMSLGKPAASLAVHTDKVQTLQFHPFEAQTLISGSYDKSVALYDCRSPEESRRMWRFSGQIERVTW
          VILWDMSLGKPAASLAVHTD.VQ.LQFHPFEAQTLISGSYDKSVALYDC.SPEESR.MWRFSGQIERVTW
Retrocopy VILWDMSLGKPAASLAVHTDEVQNLQFHPFEAQTLISGSYDKSVALYDCGSPEESRHMWRFSGQIERVTW

Parental  NHFSPCHF-LASTDDGFVYNLDARSDKPVFTLNAHNDEISGLDLSSQIKGCLVTASADKYVKIWDILGDR
          NHFS..HF.LASTDDGFVYNLDA.SDKP.FTLNAHNDEIS.LDLSSQIKGCLV.ASADKYVKIWDIL.DR
Retrocopy NHFSFFHF<LASTDDGFVYNLDACSDKPIFTLNAHNDEISCLDLSSQIKGCLVIASADKYVKIWDILDDR

Parental  PSLVHSRDMKMGVLFCSSCCPDLPFIYAF
          PSLVHSR.MKMGVLFCSSCCPDLPFI..F
Retrocopy PSLVHSRGMKMGVLFCSSCCPDLPFICLF

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_3444 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000015544	1 retrocopy	retro_mmul_688,
Macaca mulatta	ENSMMUG00000031574	1 retrocopy	retro_mmul_687,
Mus musculus	ENSMUSG00000001785	2 retrocopies	retro_mmus_1600, retro_mmus_3074,
Otolemur garnettii	ENSOGAG00000011940	2 retrocopies	retro_ogar_2999, retro_ogar_3444 ,
Rattus norvegicus	ENSRNOG00000005350	1 retrocopy	retro_rnor_646,
Tursiops truncatus	ENSTTRG00000011036	1 retrocopy	retro_ttru_540,