RetrogeneDB ID: retro_ogar_2999

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873694.1:1200195..1200954(+)
• Located in intron of: None

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_2999
AGTTCCTCAGCAGAAGAGCATACTGATGCTGTCCTTGATCTTTCATGAAATAAGCTAATCAGAAATGTATTGGCAAGTGC
ATCAGCTGATAATACTGTCATTCTGTGGGATATGTCCCTGGGGAAGCCAGCAGCTAGCCTTACTGTACACACGGATAAGG
TCCAGACTTTGCCGTTTCATCCATCTGAAACACAAACTCTGATTTCTGAATCTTATGATGAATCCGTTGCTTAGTGTGAC
TGCCTAAGTCCAGAGGAAAGCCCTCGGATGTGGCAGTTCAGTGGGCAGATCGAGAGGGTGACTTGGAATCACTTTTCACC
TTGTCACTTTTCGGCCAGTACAGATGATGGCTTTGTATATAATTTGGATGCACGTTCAGATAAGCCAATTTTTACTCTTA
ATGCCCACAATGATGAAATCTCTGGCCTTGATCTAAGCAGTCAAATCAAGGGTTGTCTTGTGACTGCTTCAGCTGACAAA
TATGTGAAGATCTGGGATATCTTAGGTGATAGGCCACGTCTAGTTCATTCTAGGGACATGAAAATGGGAGTTCTCTTCTG
TCCTTCGTGTTGCCCTGATTTGCCATTCATTTATGCCTTTGGAGGTTAGAAATAAGGGTTTAGGGTCTTGGATATAAGCA
CAGTCTCTTCAATAAATGAAGCATTTAGAAGAAGAGAGAGGCTTGTTCTCAGTAACACAAGAAATTCCTCTATTAATGGC
CTTTTGGGGAGCAGGAGCTCAGACATACCAATAGAGTCT

Alignment

ORF - retro_ogar_2999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 50.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSSAEGHTDAVLDLSWNKLIRNVLASASADNTVILWDMSLGKPAASLAVHTDKVQTLQFHPFEAQTLISG
          SSSAE.HTDAVLDLS.NKLIRNVLASASADNTVILWDMSLGKPAASL.VHTDKVQTL.FHP.E.QTLIS.
Retrocopy SSSAEEHTDAVLDLS*NKLIRNVLASASADNTVILWDMSLGKPAASLTVHTDKVQTLPFHPSETQTLISE

Parental  SYDKSVALYDCRSPEESRRMWRFSGQIERVTWNHFSPCHFLASTDDGFVYNLDARSDKPVFTLNAHNDEI
          SYD.SVA..DC.SPEES.RMW.FSGQIERVTWNHFSPCHF.ASTDDGFVYNLDARSDKP.FTLNAHNDEI
Retrocopy SYDESVA*CDCLSPEESPRMWQFSGQIERVTWNHFSPCHFSASTDDGFVYNLDARSDKPIFTLNAHNDEI

Parental  SGLDLSSQIKGCLVTASADKYVKIWDILGDRPSLVHSRDMKMGVLFCSSCCPDLPFIYAFGGQKEGLRVW
          SGLDLSSQIKGCLVTASADKYVKIWDILGDRP.LVHSRDMKMGVLFC.SCCPDLPFIYAFGG.K.G.RV.
Retrocopy SGLDLSSQIKGCLVTASADKYVKIWDILGDRPRLVHSRDMKMGVLFCPSCCPDLPFIYAFGG*K*GFRVL

Parental  DISTVSSVNEAFGRRERLVLSNIRNSSINGPLGSRSSDTPMES
          DISTVSS.NEAF.RRERLVLSN.RNSSING.LGSRSSD.P.ES
Retrocopy DISTVSSINEAFRRRERLVLSNTRNSSINGLLGSRSSDIPIES

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_2999 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,