RetrogeneDB ID: retro_ogar_2151

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873596.1:6945780..6946436(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000031071
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GID4
• Ensembl ID: ENSOGAG00000025722
• Aliases: None
• Description: GID complex subunit 4, VID24 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28453]

Sequence

>retro_ogar_2151
ATGCTGGTCCATACTGACTGTCCCCCGCCAACTGGGGCCTTGGCTGCCTCCGTGGCTTCACTCATCCCACCACCACCCAT
CAACACCCAGCAGCCGGCCCTGGCCACCAGCTTGCCCCACAGCAGCTCCAAGTTCTGTGGCCACCAGAAGAGCAAGGGGA
ACTGGTACGACGTAGAGGTGGTGCTGCAGCATGTGGACACAGGGAACTCCTGCCTTTGTGGGTCCCTGAAGATTAAAGGC
CTTACAGGGGAGTACCCAACACTTACAACCTTCTTTGAAGGACAAATAATCAGCAAAAACACCCTTTCTTCACTCAAAAG
TGGGATGCAGATGAAGTTGATCGGAATCACCAGAGAAAGTTGCTGGCTTTTGATCAGTATGCAAAATCGTTTAACTCACG
TGACTTCTGAGTTTGAAGACTATGAAGAGCTGAAGAACAGGGACTATGTCTTCATGAGGTGGAAGGAGCAGTTCCTGGTT
CCAGATCGCACAATCAAAGACATCAGTGGCACTTCCTTTGCTGGGTTCTACCACATCTGCTTTCAGAAGTCAGCAGCCTC
CATGGAGGGCAACACTGTCATAGGAGTTCAGGATGGTATCAATCTCTCAATCTAACCCATGTCCCTGAACGCAGCACACC
TATCTATGAATTCCAG

Alignment

ORF - retro_ogar_2151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPVRTECPPPAGASAASAASLIPPPPINTQQPGVATSLLYSGSKFRGHQKSKGNSYDVEVVLQHVDTGNS
          M.V.T.CPPP.GA.AAS.ASLIPPPPINTQQP..ATSL..S.SKF.GHQKSKGN.YDVEVVLQHVDTGNS
Retrocopy MLVHTDCPPPTGALAASVASLIPPPPINTQQPALATSLPHSSSKFCGHQKSKGNWYDVEVVLQHVDTGNS

Parental  YLCGYLKIKGLTEEYPTLTTFFEGEIISK-KHPFLTRKWDADEDVDRKHWGKFLAFYQYAKSFNSDDF-D
          .LCG.LKIKGLT.EYPTLTTFFEG.IISK.KHPF.T.KWDADE.VDR.H..K.LAF.QYAKSFNS.DF..
Retrocopy CLCGSLKIKGLTGEYPTLTTFFEGQIISK<KHPFFTQKWDADE-VDRNHQRKLLAFDQYAKSFNSRDF>E

Parental  YEE---LKNGDYVFMRWKEQFLVPDHTIKDISGASFAGFYYICFQKSAASIE-GYYYHRSSEWYQSLNLT
          .E....LKN.DYVFMRWKEQFLVPD.TIKDISG.SFAGFY.ICFQKSAAS.E.G...HRSS.WYQSLNLT
Retrocopy FEDYEELKNRDYVFMRWKEQFLVPDRTIKDISGTSFAGFYHICFQKSAASME<GQHCHRSSGWYQSLNLT

Parental  HVPEHSAPIYEFR
          HVPE.S.PIYEF.
Retrocopy HVPERSTPIYEFQ

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_2151 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	ENSOGAG00000025722	1 retrocopy	retro_ogar_2151 ,