RetrogeneDB ID: retro_ogar_938

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:33318321..33318839(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GIPC2
• Ensembl ID: ENSOGAG00000007256
• Aliases: None
• Description: GIPC PDZ domain containing family, member 2 [Source:HGNC Symbol;Acc:18177]

Sequence

>retro_ogar_938
TTTATAAAGAGAATTAAAGATGGTGACATTATTCACTCGGTCCAAAACATTCATGTGGGAGATCATATTGAATGTGAGAG
TATTGTTGGTTGGCATCACTATGCTGTTGCTATGAAGTTAAAGGAATTGGAAAAAGGTGAACAGTTTACCATGAAGTTAA
TAGAACCTAAGAAGGGATTTGAAATAGAGCTGAGGCCAAAAGCTGGAAAGTCATTAGCAGAAAAGTTACCAGAAGGAGGA
AAATTTACTAGAGAGAAACTCTTCACCTGAGGTCAAAAGGACCTGTAAACATAGAAGAAATGCCTTCTGGAGCCAAAGCA
AAGGCAATTGAAAGGATTGATGACGTTCTTGAACTGTACATGGGAATTTGAGATGCTGACTTAGCTACCGAAATGTTTGA
ATCTGGAAAGGACAAAAGTACTTCAGAAAAACTTGGCACAGAACCCAACAAAATTCTTGGAGACTCTGTATTCCCAGAAG
ATGTTGTCGTTTCTGTTTGAAAGGTCATTGGTGATGCC

Alignment

ORF - retro_ogar_938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.16 %
• Parental protein coverage: 55.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FIKRIRDGGIIYLVQTICVGDHIESINGESVVGWRHYAVAQKFKELKKWEYFTMKLIEPKKASEMQLRSK
          FIKRI.DG.II..VQ.I.VGDHIE....ES.VGW.HYAVA.K.KEL.K.E.FTMKLIEPKK..E..LR.K
Retrocopy FIKRIKDGDIIHSVQNIHVGDHIEC---ESIVGWHHYAVAMKLKELEKGEQFTMKLIEPKKGFEIELRPK

Parental  PGKSSVEKLP-GGTFTRKK-SLRLRSKGPAKIEEKIKPSGAEAKAIERIDDLLELYMGIQDADLATEIFE
          .GKS..EKLP.GG.FTR.K..L.LRSKGP..IEE...PSGA.AKAIERIDD.LELYMGI.DADLATE.FE
Retrocopy AGKSLAEKLPEGGKFTREK<TLHLRSKGPVNIEEM--PSGAKAKAIERIDDVLELYMGI*DADLATEMFE

Parental  AGKDKGTSEELGKALKEVLEDFVFPEEVVPDVWKAICDA
          .GKDK.TSE.LG......L.D.VFPE.VV..V.K.I.DA
Retrocopy SGKDKSTSEKLGTEPNKILGDSVFPEDVVVSV*KVIGDA

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_938 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
Macropus eugenii	ENSMEUG00000010616	1 retrocopy	retro_meug_464,
Otolemur garnettii	ENSOGAG00000007256	1 retrocopy	retro_ogar_938 ,