RetrogeneDB ID: retro_ogar_3019

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873697.1:1780411..1781023(-)
• Located in intron of: ENSOGAG00000005633

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPCS
• Ensembl ID: ENSOGAG00000031647
• Aliases: None
• Description: phosphopantothenoylcysteine synthetase [Source:HGNC Symbol;Acc:25686]

Sequence

>retro_ogar_3019
TCCAGCCCAGCCCATTCGGGCTTGCTGAGCCTTGAGGCCGAGGAGAATGCACTCCCGGGCTTCGCTGCGGCTTTGCGAAA
CTACCGGGAGGCTGTGGCTGCCGGTACTTTTCTGGCGGTAGAGTTCACCACTGTGGTGGACTATTTACATTTGTTGCAGG
CTGCAGCCTAGGCGCTCAATCCGCTAGGCTCTTCTGCGATGTTTTACCTGGCTGCGGCCGTGTCAGATTTCTATGTTCCT
GTCTCTGAAATGCCTGAACACAAGATCCAGTCATCTGGGGGCCTATTGCAGATAACAATGAAGATGGTGCCAAAAATGCT
TTCTCCTTTGGTTAAAGATTGGGCTCCAAAAGCATTTATAATTTCCTTCAAGTTGGAGACTGACCCCTCCATTGTAATTA
CTCGTGCTCGGAACGCTTTGGAAGTTTATCAACATCAAGTGGTGGTGGCTAATATCCTTGAGTCACGACAGTCATTTGTG
GTTACTATAACCAAAGACTCAGAAACCAAGTTATTGCTATCAGAAGAAGAAGTAGAAAAAGGCATAGAGATAGAAGAGAA
GATAGTGGATAATCTTCGGTCTCGACACACAGCTTTTATATGTGACAAAAAC

Alignment

ORF - retro_ogar_3019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.57 %
• Parental protein coverage: 65.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGPAHSGLLSLEAEENALPGFAAALRNYQEAVAAGTFLAVEFTTVADYLHLLQAAAHALNPLGSSAMFYL
          S.PAHSGLLSLEAEENALPGFAAALRNY.EAVAAGTFLAVEFTTV.DYLHLLQAAA.ALNPLGSSAMFYL
Retrocopy SSPAHSGLLSLEAEENALPGFAAALRNYREAVAAGTFLAVEFTTVVDYLHLLQAAA*ALNPLGSSAMFYL

Parental  AAAVSDFYVPVSEMPEHKIQSSGGLLQITMKMVPKMLSPLVKDWAPKAFIISFKLETDPSIVINRARNAL
          AAAVSDFYVPVSEMPEHKIQSSGGLLQITMKMVPKMLSPLVKDWAPKAFIISFKLETDPSIVI.RARNAL
Retrocopy AAAVSDFYVPVSEMPEHKIQSSGGLLQITMKMVPKMLSPLVKDWAPKAFIISFKLETDPSIVITRARNAL

Parental  EVYQHQVVVANILESRQSFVVIVTKDSETKLLLSEEEVEKGIEIEEKIVDNLRSRHTAFICDKN
          EVYQHQVVVANILESRQSFVV..TKDSETKLLLSEEEVEKGIEIEEKIVDNLRSRHTAFICDKN
Retrocopy EVYQHQVVVANILESRQSFVVTITKDSETKLLLSEEEVEKGIEIEEKIVDNLRSRHTAFICDKN

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_3019 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028636	1 retrocopy	retro_mmus_1542,
Otolemur garnettii	ENSOGAG00000031647	1 retrocopy	retro_ogar_3019 ,