RetrogeneDB ID: retro_ogar_2852

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873672.1:3747133..3747872(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOTO
• Ensembl ID: ENSOGAG00000034740
• Aliases: None
• Description: notochord homeobox [Source:HGNC Symbol;Acc:31839]

Sequence

>retro_ogar_2852
GCTGGGGTACAGCCCCCGCGCGTGGGCAGCTCCCCAGCGCCTCAGTCTCCCGCGCTCTTGGACCACCCCGCCGGCCGCGG
AAAGCCCAGAGCGCCTGGACGCCTCGAGTTCTTCTCTGTCCAGGCAATCCTGGTGAGGCTGGATCCTAGCGCTCAGGCTG
TCTCCCAGATGTCAGGCTCCGCGGGCACCTTCCTGGGTCTCCGGACTGCTCCATCCCAGTGTCTTGTCCGGGTTCTGTCC
TGGGTGTGCCTGATGCCTTGGCTGCCCGCCTACCTGAGCATGAGTCTCTACCAGCTGTACTCCCAGCAGCCTGTGCAGGG
GCTGCGCCTGGTTCATTTCTGCGGCCTCCAGGGCGTCCGGGACACAGGTTTGGAGCTAGCTTACCGTCCAGGCCTCTGGA
GCCCCCCAAGACTGAGTCCCAACTAAGGACCTTCCAGACACCGAGAGACACCAAAAGAGGGTCTGAACTATGTTTAACTT
GCAGCAGCTGGAAGAGCTGGAGAAGGTGTTTGCCAAACAGCACAATCTGGTGGGGAAGAAGAGAGCCCAGCCGGCAGCCC
GGGTCAACCTTACAGAGAACCAGATAAGGATCTGGTTCCAGAATCTCAGGGTCAAGTATCAGAGACAGCAAAAGCTGAGA
CTGCCGGCTGCATCTGCCAAGGCTGCCTCCCTGGACAAGTGCTCCAGAAGCTCCAATGCTAGCATCCAGAGTGATGACTG
TGAGTCAGGAGTGGACAGC

Alignment

ORF - retro_ogar_2852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 93.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGVRPPRAGSSTAPRSPALLDRPAGGEKPRAPGRLESFSVEAILARPDPRAPAVSQLSGSAGTFQGLWTA
          AGV.PPR.GSS.AP.SPALLD.PAG..KPRAPGRLE.FSV.AIL.R.DP.A.AVSQ.SGSAGTF.GL.TA
Retrocopy AGVQPPRVGSSPAPQSPALLDHPAGRGKPRAPGRLEFFSVQAILVRLDPSAQAVSQMSGSAGTFLGLRTA

Parental  PSQCPVPVLPWVCPAPWLPAYLSMSLYPLYPQQPVQGLRLAHFCGLQGVGDTDLELAYRPGLRSSP-DWV
          PSQC.V.VL.WVC..PWLPAYLSMSLY.LY.QQPVQGLRL.HFCGLQGV.DT.LELAYRPGL.S.P.D.V
Retrocopy PSQCLVRVLSWVCLMPWLPAYLSMSLYQLYSQQPVQGLRLVHFCGLQGVRDTGLELAYRPGLWSPP>D*V

Parental  PTKDLPDTERYQKRVRTMFNLEQLEELEKVFAKQHNLVGKKRAQLAARLNLTENQVRVWFQNRRVKYQKQ
          PTKDLPDTER.QKRV.TMFNL.QLEELEKVFAKQHNLVGKKRAQ.AAR.NLTENQ.R.WFQN.RVKYQ.Q
Retrocopy PTKDLPDTERHQKRV*TMFNLQQLEELEKVFAKQHNLVGKKRAQPAARVNLTENQIRIWFQNLRVKYQRQ

Parental  QKVRLPAASAEAASLDEPSSSSNASIQSDDFESGVDS
          QK.RLPAASA.AASLD..S.SSNASIQSDD.ESGVDS
Retrocopy QKLRLPAASAKAASLDKCSRSSNASIQSDDCESGVDS

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_2852 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000034740	1 retrocopy	retro_ogar_2852 ,