RetrogeneDB ID: retro_ogar_332

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:30833747..30834275(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHAC2
• Ensembl ID: ENSOGAG00000010331
• Aliases: None
• Description: ChaC, cation transport regulator homolog 2 (E. coli) [Source:HGNC Symbol;Acc:32363]

Sequence

>retro_ogar_332
ATGTGGGTATTTGATTACGGGTCCCTGATCTGGAAGGTGGACTTCCCCTATCAGGACAAGCTGGTTAGATCCATCACAAA
CTACAGCAGGCTCTTCTGGCAGGGCAGCACAGACCACCATGGGGTCCCTGGTGAGCCTGGAAGAGTGGTGACTCTTGTTG
AAGATCCTGGGGGTTGTGTATGGGGTGTAGCTTACAAATTGCCAATAGGAAAGGAAGAAGAAGTAAAAGCATACCTTGAC
TTTAGAGAGAAAGGAGGCTAAAGGACCACAACGGTCATTTTTTATCCAAAAGATTCCACAACAAATCCATTCAGTGTGTT
GCTATATATTGGAACATGTGATAATCCTAATTACCTTGGTCCTGCACCACTGGAAGACATTGCTGAATAATTTTTTAATG
CAGCTGGTCCAAGTGGAAGAAATACAGAGCATCTTATTGAATTTACCAATTCTATTAGGAACCTTTTGCCAGAAGATGCA
GATGAGCATCTTTTCTCTTTGGAAAAATTAGTAAAGGAACGTTTAGAA

Alignment

ORF - retro_ogar_332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.34 %
• Parental protein coverage: 95.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWVFGYGSLIWKVDFPYQDKLVGYITNYSRRFWQGSTDHRGVPGKPGRVVTLVEDPGGCVWGVAYKLPMG
          MWVF.YGSLIWKVDFPYQDKLV..ITNYSR.FWQGSTDH.GVPG.PGRVVTLVEDPGGCVWGVAYKLP.G
Retrocopy MWVFDYGSLIWKVDFPYQDKLVRSITNYSRLFWQGSTDHHGVPGEPGRVVTLVEDPGGCVWGVAYKLPIG

Parental  KEEEVKAYLDFREKGGYRTTTVVFYPKDSTTKPFSVLLYIGTCDNPNYLGPAPLEDIAEQIFNAAGPSGR
          KEEEVKAYLDFREKGG.RTTTV.FYPKDSTT.PFSVLLYIGTCDNPNYLGPAPLEDIAE..FNAAGPSGR
Retrocopy KEEEVKAYLDFREKGG*RTTTVIFYPKDSTTNPFSVLLYIGTCDNPNYLGPAPLEDIAE*FFNAAGPSGR

Parental  NTEYLFELANSIRNLVPEDADEHLFSLEKLVKERLE
          NTE.L.E..NSIRNL.PEDADEHLFSLEKLVKERLE
Retrocopy NTEHLIEFTNSIRNLLPEDADEHLFSLEKLVKERLE

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_332 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000010331	1 retrocopy	retro_ogar_332 ,
Otolemur garnettii	ENSOGAG00000024541	1 retrocopy	retro_ogar_3206,
Rattus norvegicus	ENSRNOG00000001531	1 retrocopy	retro_rnor_822,