RetrogeneDB ID: retro_ogar_1578

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873553.1:5601062..5601655(+)
• Located in intron of: ENSOGAG00000004472

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUS4L
• Ensembl ID: ENSOGAG00000013113
• Aliases: None
• Description: dihydrouridine synthase 4-like (S. cerevisiae) [Source:HGNC Symbol;Acc:21517]

Sequence

>retro_ogar_1578
TGGGCAATGGCAGAAGGTTATGGGGCTTGCTTAATAAACAAGCCAGAGCTTGTTCAAGATATGATGTAACAAGTAAGAAA
TCAAGTGGGAAACCCTAGATTTTCAGTTTCTATTAAAATAAGGATCCATGATGACCTTTCAAGAACTGTAGATGTTTGTC
GAAAAGCTGAAGCTATAGGAGTTTCCTGGATCACAGTTCATGGAAGAACTACTGAAGAAAGACATCAGCCAGTGCACTAT
GATGCCATTAAAATAATTAAGGAGAATATGTCTATACTTGTAATTGCTAATGGAGACATCAGAAGCTTAAAAGAAGCAAA
AAATGTGTGGCAGAATACTGGGACAGATGGTGTGATGGTTGCAAGAGGATTCTTAGCAAACCCGGCCATGTTTGCTGGAT
TTGAGGAAACCCCACTGAAGTGCATCTGGGACTGGGCTGGCATTGCTCTGAACTTGGAACTCCTTACATGTGTTTCCATC
AACATTTAATGTACATGATGGAAAAGATAACTTCTAGGCAGGAAAAAAGAGTATTTAATGCTCTGTCAAGCACATCAGCA
GTCTTAGATTACCTTACAGACCATTATGGCATT

Alignment

ORF - retro_ogar_1578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.97 %
• Parental protein coverage: 61.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WAMAEGYGACLINKPELVQDMVKQVRNQVGNPRFSVSIKIRIHDDLSRTVDLCRKAEATGVSWITVHGRT
          WAMAEGYGACLINKPELVQDM..QVRNQVGNPRFSVSIKIRIHDDLSRTVD.CRKAEA.GVSWITVHGRT
Retrocopy WAMAEGYGACLINKPELVQDMM*QVRNQVGNPRFSVSIKIRIHDDLSRTVDVCRKAEAIGVSWITVHGRT

Parental  TEERHQPVHYDAIKIIKENMSIPVIANGDIRSLKEAENVWQNTGTDGVMVARGLLANPAMFAGFEETPLK
          TEERHQPVHYDAIKIIKENMSI.VIANGDIRSLKEA.NVWQNTGTDGVMVARG.LANPAMFAGFEETPLK
Retrocopy TEERHQPVHYDAIKIIKENMSILVIANGDIRSLKEAKNVWQNTGTDGVMVARGFLANPAMFAGFEETPLK

Parental  CIWDWVDIAL-ELGTPYMCFHQHLMYMMEKITSRQEKRVFNALSSTSAVLDYLTDHYGI
          CIWDW..IAL.ELGTPYMCFHQHLMYMMEKITSRQEKRVFNALSSTSAVLDYLTDHYGI
Retrocopy CIWDWAGIAL<ELGTPYMCFHQHLMYMMEKITSRQEKRVFNALSSTSAVLDYLTDHYGI

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_1578 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006848	1 retrocopy	retro_chof_1283,
Cavia porcellus	ENSCPOG00000002384	1 retrocopy	retro_cpor_701,
Otolemur garnettii	ENSOGAG00000013113	2 retrocopies	retro_ogar_1578 , retro_ogar_894,