RetrogeneDB ID: retro_ogar_1338

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873543.1:20314417..20315266(+)
• Located in intron of: ENSOGAG00000026615

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSOGAG00000004068
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_ogar_1338
GCTGTGAACGGGGCGGCGGGCGTCTCAAGCTCGGGGCCTGCCGCGACGCCTGGCACTGTCCTGCAGGCTGCGGCTGGCAT
TTACGAGCAACTTAAGGGCGAGTGGAACTGTAAAAGCCCCAATCTTAGCAAGTGCGGGGAAGAGCTGGGGTGCCTCAAGC
TAGTTCTGCTGGAGCTCAACTTCCTTCCAACCACAGGCACCAAGCTGACCAAACAGCAGCTCATTCTGGCCCATGACATA
CTGGAGATCCGGGCCCAGTGGAGCATCTTGCGAAAGGACATCCTCTCCTTCAAGCGCTACATGGCGCAGCTCAAATGCTA
CTACTTTGATTATAAGGAGCAGCTCCCTGAGTCAGCCTAAATGCACCAACTCTTGGGCCTCAATCTTCTCTTCCTGCTGT
CCCAGAACCGGGTGGCTGAGTTTTACACGGAATTGGAGCAGCTGCCTGCCAAGGACATTCAGACCAATGTCTACATCAAG
CACCCTGTGTCCCTTGAGCAATACCTGATGGAAGGCAGCTACAACAAGGTGTTCCTGGCCAAGGGGAACATCCCTGCTGA
GAGTTACACTTTCTTCATTGACATCCTACTTGACACTATCAGGGATGAGATTGCTGGATGCATCGAGAAGGCCTATGAGA
AAATCCTTTTCACTGAGGCCACCTGGATCCTCTTCTTCAACACACCCAAAAAGATGACAGACTATGCCAAGAAGCGAGGG
TGGGTCCTTGGCCCCCACAACTACTACAGTTTTGCCAGCCAGCAGCAGAAACCAGAAGACACCACCATTCCCTCTACAGA
ACTGGCCAAACAGGTCATTGAGTATGCCCGGCAGCTGGAGATGATCATC

Alignment

ORF - retro_ogar_1338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.41 %
• Parental protein coverage: 80.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVNGTAGVSSSGPAATPGTVLQAAAGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTTGTKLT
          AVNG.AGVSSSGPAATPGTVLQAAAG.YEQLKGEWN.KSPNLSKCGEELG.LKLVLLELNFLPTTGTKLT
Retrocopy AVNGAAGVSSSGPAATPGTVLQAAAGIYEQLKGEWNCKSPNLSKCGEELGCLKLVLLELNFLPTTGTKLT

Parental  KQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRVAE
          KQQLILA.DILEI.AQWSILRKDI.SF.RYMAQLKCYYFDYKEQLPESA.MHQLLGLNLLFLLSQNRVAE
Retrocopy KQQLILAHDILEIRAQWSILRKDILSFKRYMAQLKCYYFDYKEQLPESA*MHQLLGLNLLFLLSQNRVAE

Parental  FHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEK
          F.TELE.LPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEK
Retrocopy FYTELEQLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEK

Parental  AYEKILFTEATRILFFNTPKKMTDYAKKRGWVLGPHNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLE
          AYEKILFTEAT.ILFFNTPKKMTDYAKKRGWVLGPHNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLE
Retrocopy AYEKILFTEATWILFFNTPKKMTDYAKKRGWVLGPHNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLE

Parental  MIV
          MI.
Retrocopy MII

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_1338 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
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Otolemur garnettii	ENSOGAG00000004068	1 retrocopy	retro_ogar_1338 ,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,