RetrogeneDB ID: retro_ogar_1357

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873543.1:20457599..20458293(-)
• Located in intron of: ENSOGAG00000026615

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3F
• Ensembl ID: ENSOGAG00000002916
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa [Source:HGNC Symbol;Acc:15763]

Sequence

>retro_ogar_1357
GTCACAGACTCCATGCCTTATATAGAAGCCCAGCAGCGGGCAGTGGCCATTAACAGACTGTTGTCCATGGGTCAATTGGA
CCTCTTAAGGAGCGGTACAGGCCTTTTATATAGAATAGAAGACTCTCAGAATGCTGGGAAAATGAAAGGATCAGATAACC
AAGAAAAACTAGTATATCAAATCATAGAAGATGCAGGAAATAAAGGAATATGGAGCAGAGATATCCGATACAAAAGTGAC
TTGCCATTAACAGAAGTCAACAAAATTCTGAAGAACTTGGAAAGTAAAAAACCTCATTAAAGCTGTTAAGTCTGTAGCAG
CCTCCAAAAAGAAGGTGTACATGCTCTACAACATGCAGCCAGACCGCCCTGTGACTGGAGGGGCCTGGTACAGTGACCAA
GACTTTGAATCTGAGTTTGTGGAGGTGCTTAACCACCAGTGTTTTAAATTCCTACAAACCAAGGCAGAAACAGCACAAGA
AAGCAAAAAGAATCCAGTAATACAAAGAAATAGTTCATTTGCTTCATCACATAAAGTGTGGAAATATATCTGTGAACTAG
GGATCAGTGAGGTAGAGTTGTCCATGGAGGATATTGAAACCATCCTAAATACACTCATTTATGATGGGAAAGTGAAGATG
ACTATCATTGTTGCAAAAGAAGGTACAGTTGGCAGTATAGAAGAAGAAAAGAAG

Alignment

ORF - retro_ogar_1357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 73.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQNEMPHIEAQQRAVAINRLLSMGQLDLLRSSTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGI
          ....MP.IEAQQRAVAINRLLSMGQLDLLRS.TGLLYRI.DSQNAGKMKGSDNQEKLVYQIIEDAGNKGI
Retrocopy VTDSMPYIEAQQRAVAINRLLSMGQLDLLRSGTGLLYRIEDSQNAGKMKGSDNQEKLVYQIIEDAGNKGI

Parental  WSRDIRYKSNLPLTEINKILKNLESKK-LIKAVKSVAASKKKVYMLYNMQPDRSVTGGAWYSDHDFESEF
          WSRDIRYKS.LPLTE.NKILKNLESKK.LIKAVKSVAASKKKVYMLYNMQPDR.VTGGAWYSD.DFESEF
Retrocopy WSRDIRYKSDLPLTEVNKILKNLESKK>LIKAVKSVAASKKKVYMLYNMQPDRPVTGGAWYSDQDFESEF

Parental  VEVLNQQCFKFLQTKAETARESKQNPVIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDG
          VEVLN.QCFKFLQTKAETA.ESK.NPVIQRNSSFASSH.VWKYICELGIS.VELSMEDIETILNTLIYDG
Retrocopy VEVLNHQCFKFLQTKAETAQESKKNPVIQRNSSFASSHKVWKYICELGISEVELSMEDIETILNTLIYDG

Parental  KVEMTIIAAKEGTVGSVDGHMK
          KV.MTII.AKEGTVGS.....K
Retrocopy KVKMTIIVAKEGTVGSIEEEKK

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_1357 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
Myotis lucifugus	ENSMLUG00000014844	1 retrocopy	retro_mluc_2046,
Monodelphis domestica	ENSMODG00000005624	1 retrocopy	retro_mdom_1899,
Otolemur garnettii	ENSOGAG00000002916	1 retrocopy	retro_ogar_1357 ,