RetrogeneDB ID: retro_ogar_3206

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873741.1:72281..72825(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHAC1
• Ensembl ID: ENSOGAG00000024541
• Aliases: None
• Description: ChaC, cation transport regulator homolog 1 (E. coli) [Source:HGNC Symbol;Acc:28680]

Sequence

>retro_ogar_3206
GAGCTGCAGCGGCCAAGAGGTGCCAGGCCAGGCAGGAGCGTCCGTCGGTCCTTCGGGGGCCCAAGCTGGAGTCCGCCCCA
GAGGCGGAGGCCGCCTGGCCCATCCCTGAGCCCGGCACCAGGAAGCAGAGAGCCGCGAACACCTGCCCGCATCACTGTCC
CCTCCGACCTCCGCTCCGCACCCCCGGGACCATTGCGATTCTTTGTGGATTTTCTGGTACAGCTCCCAGGTGTGCAGGCC
CGACTGCGCTTATAGCGACAGCCGAGTGGGTTTCGCGCGGTTATGGCGGCCGTTTCTGGCCAGGAGACACCTTCCATCGG
GGCAGCCACCAGATGCCTGGCCGTGTGGTGACTCTCCTTGAAGGTCATAAGGGCAGCTTTTGGGGTGTGGCATACCAAGG
GCAAGGTGAGCAAGGGAGCGAGGCTCTCAAGTCCCTGACTGTGCGGGAGGCAGTTCTCGGCGCTTAGGATGCCAAAGAAG
GCACTTTCTATCCCCAAGATACCCCTGACCAACCACGGAGGCATTGGCCTATGTGTGGCCACCC

Alignment

ORF - retro_ogar_3206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.78 %
• Parental protein coverage: 70.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QLERPSGARPGVSVRRSFRAHAGDRP--RRPPGPIPEPGTMKQESAAPNTP-PTSPSPPTSAPHPRDDSD
          .L.RP.GARPG.SVRRSF.......P..RRPPGP...P.....E...P.TP.P.S.SPPTSAPHPRD..D
Retrocopy ELQRPRGARPGRSVRRSFGGPSWSPPQRRRPPGPSLSPAPGSRE---PRTP>PASLSPPTSAPHPRDHCD

Parental  SLWIFGYGSLVWRPDFAYSDSRV-GF-VRGYSRRFWQGDTFHRGSDKMPGRVVTLLEDHKGCTWGVAYQV
          SLWIF.Y.S.V.RPD.AYSDSRV.GF..RGY..RFW.GDTFHRGS..MPGRVVTLLE.HKG..WGVAYQ.
Retrocopy SLWIFWYSSQVCRPDCAYSDSRV<GF<SRGYGGRFWPGDTFHRGSHQMPGRVVTLLEGHKGSFWGVAYQG

Parental  QGEQVSEALKYLNVREAVLGGYDTKEVTFYPQDTPDQP-LKALAYVATP
          QGEQ.SEALK.L.VREAVLG..D.KE.TFYPQDTPDQP...ALAYV..P
Retrocopy QGEQGSEALKSLTVREAVLGA*DAKEGTFYPQDTPDQP<TEALAYVWPP

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_3206 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017531	1 retrocopy	retro_dnov_438,
Otolemur garnettii	ENSOGAG00000010331	1 retrocopy	retro_ogar_332,
Otolemur garnettii	ENSOGAG00000024541	1 retrocopy	retro_ogar_3206 ,
Tursiops truncatus	ENSTTRG00000011476	2 retrocopies	retro_ttru_1747, retro_ttru_945,