RetrogeneDB ID: retro_ogar_1252

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873540.1:24805920..24806698(+)
• Located in intron of: ENSOGAG00000003757

Retrocopy information

• Ensembl ID: ENSOGAG00000032988
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DPM1
• Ensembl ID: ENSOGAG00000005384
• Aliases: None
• Description: dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit [Source:HGNC Symbol;Acc:3005]

Sequence

>retro_ogar_1252
ATGGCCTCCTCCGAAGCCAGTCGTTCTTCTCCCTGGTCTCCGTGGGAGCTAGAAGTGCGCAATCCACGCCAGGACAAGTA
TTCTGTGCTTTTGCCCGCCTACAATGAGTGCAAGAACTACCACTCATCGTGTGGCGGCTGGTGAAAAGCTTCTCGGAGAG
CGGCATCAACTATGAAGTTATAATTATAGATGATGGAAGCCCAGATGGAACAAGGGACGTTGCTGAACAGTTGGAGAAGA
TTTACGGGGCAGACAGAATCCTACTAAGACCACGAGAGAAAAAGTTGGGGCTAGGGACTGCATATATTCATGGAATGAAA
CGTGCCACGGGAAACTACATAATTATTATGGACGCTGATCTCTCACACCATCCAAAATTCATTCCTGAATTCTTTAGGAA
GCAGAAGGAGGGTAACTTTGATATTGTCTCTGGAACTCACTACAAAGGAAGTGGAGGTGTATATGGCTGGGATTTGAAAA
GAAAAATAATCAGCCATGGAGCCAATTTCATAACACAGATTTTGCTGAGACCAGGAGCATCTGATTTAACAGGAAGTTTC
AGATTATACTGCAAAGAAGTTCTACAGAAATTAATAGAAAAATGTGTTTCTAAAGGCTATGTCTTCCAGATGGGATGATT
GTTCCGGCAAGACAGTTGAATTATACTGTTGGTGAGGTTCCAGTATCATTTCTGGATCGAGTTTATGGTGAATCCAAGCT
GGGAGGAAATGAAATAGTCTCTTTCTTGAAAGGCTTATTGACTCTCTTTGCTACTACA

Alignment

ORF - retro_ogar_1252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASSEASRSSPRSRRELEVRNPRQDKYSVLLPTYNEREN-LPLIVWLLVKSFSESGINYEVIIIDDGSPD
          MASSEASRSSP.S..ELEVRNPRQDKYSVLLP.YNE..N.LPLIVW.LVKSFSESGINYEVIIIDDGSPD
Retrocopy MASSEASRSSPWSPWELEVRNPRQDKYSVLLPAYNECKN<LPLIVWRLVKSFSESGINYEVIIIDDGSPD

Parental  GTRDVAEQLEKIYGADRILLRPREKKLGLGTAYIHGMKHATGNYIIIMDADLSHHPKFIPEFIRKQKEGN
          GTRDVAEQLEKIYGADRILLRPREKKLGLGTAYIHGMK.ATGNYIIIMDADLSHHPKFIPEF.RKQKEGN
Retrocopy GTRDVAEQLEKIYGADRILLRPREKKLGLGTAYIHGMKRATGNYIIIMDADLSHHPKFIPEFFRKQKEGN

Parental  FDIVSGTRYKGSGGVYGWDLKRKIISRGANFITQILLRPGASDLTGSFRLYRKEVLQKLIEKCVSKGYVF
          FDIVSGT.YKGSGGVYGWDLKRKIIS.GANFITQILLRPGASDLTGSFRLY.KEVLQKLIEKCVSKGYVF
Retrocopy FDIVSGTHYKGSGGVYGWDLKRKIISHGANFITQILLRPGASDLTGSFRLYCKEVLQKLIEKCVSKGYVF

Parental  QM-EMIVRARQLNYTIGEVPISFVDRVYGESKLGGNEIVSFLKGLLTLFATT
          QM..MIV.ARQLNYT.GEVP.SF.DRVYGESKLGGNEIVSFLKGLLTLFATT
Retrocopy QM<GMIVPARQLNYTVGEVPVSFLDRVYGESKLGGNEIVSFLKGLLTLFATT

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_1252 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000005384	2 retrocopies	retro_ogar_1252 , retro_ogar_2283,