RetrogeneDB ID: retro_ogar_495

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873522.1:42990633..42991824(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029982
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLR1E
• Ensembl ID: ENSOGAG00000012981
• Aliases: None
• Description: polymerase (RNA) I polypeptide E, 53kDa [Source:HGNC Symbol;Acc:17631]

Sequence

>retro_ogar_495
CGCACTCTTACAGTCCAGTTCTCCAATGGGAAGCTTTAGAATCCAGGCAACATGCGCTTTACCTTATACAAAAGCACCGA
CGCCAAAAACCCCAGGAGGAGAAATTAGCGGATCCTGGCAGCTTGAACAGACAGACTTTCCTATGTGGGAAATAATTTTG
GGACTGGAGCCCTGAAACGCAACACTCTATGCAGGCACTTTGTAGGAATATTGAACAAGACCTCTGGCCAAATGGAAGTG
TTTGATGCGGAACTGTTGAACATGCAGCCACTGTTTTCAGATGAATCAGTTGAGACTGAACAGACACTAGACAGCCAGAC
CAAAACTTTCAGAGAAAAGATGGATTCTTGTATTGAAGCCTTTGGTACCACCAAACAGAAGTGAGCGCTGAACTCCAGAA
GAATGAACAGGGTTGGCAATGAATCTTTGAATCTTGCAGTAGCTAAAGCTGCAGAGAATATCACTGATACAAAGATTGTG
ACTGCTCTGGTCTGTGATGCCATCCATGATGACTTGCAAGATGACTCCCTCTACCTTCCTCCCTGCCATGCCGATGCAGC
CAAGCCTGAAGATGTGTATAAATTTGAAGATCTTCTTTCTCCTGTGGAGTATGAAGCTCTTCAGAGCCCATCTGAAGCTT
TCAGGAATGTCACATCAGAAGAGATACTGAAGATGATTGAAGAGAACAGCCACTGCTCCTTTGTCATAGAAGCACTGAAG
TCTTTGCCATCAAACGAGGAGAGCTGAGATCGGCAGGCCTGATGCATATGGTTTCTGGATACCCTCATCAAATTTCGAAC
TCAGAGAGTGATTAAGCGGAAAAGTGCCCTGGGACCTGGAGTGCCACACATCAACACCAAGCTGCTGAAGCACTTCCCCT
GCCTGACTTACAACAATGGCAGTTTGCATAACTTAATTTTGGATTCTATGAAGGCGAAGATTACTGCATATGTGATCATA
CTTGCCTTGCACATAAGCAGCTTCCAGATTGACCTGACGACGTTACAGAGGGACTTAAAGCTCAGTGAGAGAAGGATGAT
GGAGATAGTAAGAGCCATGAGGCTGACGATCTCTAAAAGAAGGGTGTCTCTGGCTGCTGGTGGGGAAGAAGATCACAAAC
TGGGCACTCTGTCCATCCCACTGCCTCCAGCACAGACCTCAGACCGCCAGTCAAAGCGGAGGAAAATTACC

Alignment

ORF - retro_ogar_495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.46 %
• Parental protein coverage: 92.77 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAVLVQFSNGKLQNPGNMRFTLYKSDDSKNPRRKNQRILAAETDRLSYVGNNFGTGALKCNTLCRHFVGI
          R...VQFSNGKL.NPGNMRFTLYKS.D.KNPRR.N.RILAA.TDRLSYVGNNFGTGALK.NTLCRHFVGI
Retrocopy RTLTVQFSNGKL*NPGNMRFTLYKSTDAKNPRRRN*RILAA*TDRLSYVGNNFGTGALKRNTLCRHFVGI

Parental  LNKTSGQMEVYDAELFNMQPLFSDESVETEQTLDSQTKTFREKMDSCIEAFGTTKQKRALNSRRMNRVGN
          LNKTSGQMEV.DAEL.NMQPLFSDESVETEQTLDSQTKTFREKMDSCIEAFGTTKQK.ALNSRRMNRVGN
Retrocopy LNKTSGQMEVFDAELLNMQPLFSDESVETEQTLDSQTKTFREKMDSCIEAFGTTKQK*ALNSRRMNRVGN

Parental  ESLNLAVAKAAENIIDTKGVTALVSDAIHDDLQDDSLYLPPCHADAAKPEDVYKFEDLLSPVEYEALQSP
          ESLNLAVAKAAENI.DTK.VTALV.DAIHDDLQDDSLYLPPCHADAAKPEDVYKFEDLLSPVEYEALQSP
Retrocopy ESLNLAVAKAAENITDTKIVTALVCDAIHDDLQDDSLYLPPCHADAAKPEDVYKFEDLLSPVEYEALQSP

Parental  SEAFRNVTSEDILKMIEENSHCSFVIEALKSLPSNEESRDRQARCIWFLDTLIKFRTQKVIKRKSALGPA
          SEAFRNVTSE.ILKMIEENSHCSFVIEALKSLPSNEES.DRQA.CIWFLDTLIKFRTQ.VIKRKSALGP.
Retrocopy SEAFRNVTSEEILKMIEENSHCSFVIEALKSLPSNEES*DRQA*CIWFLDTLIKFRTQRVIKRKSALGPG

Parental  VPHIINTKLLKHFTCLTYNNGSLRNLISDSMKAKITAYVIILALHISSFQIDLTMLQRDLKLSERRMMEI
          VPH.INTKLLKHF.CLTYNNGSL.NLI.DSMKAKITAYVIILALHISSFQIDLT.LQRDLKLSERRMMEI
Retrocopy VPH-INTKLLKHFPCLTYNNGSLHNLILDSMKAKITAYVIILALHISSFQIDLTTLQRDLKLSERRMMEI

Parental  ARAMRLKISKTRVSLAAGGEEDHKLGTLSIPLPPAQTSDRQSKRRRIT
          .RAMRL.ISK.RVSLAAGGEEDHKLGTLSIPLPPAQTSDRQSKRR.IT
Retrocopy VRAMRLTISKRRVSLAAGGEEDHKLGTLSIPLPPAQTSDRQSKRRKIT

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_495 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012688	1 retrocopy	retro_mluc_2497,
Otolemur garnettii	ENSOGAG00000012981	1 retrocopy	retro_ogar_495 ,