RetrogeneDB ID: retro_ogar_1564

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873551.1:9001067..9001780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIH1D1
• Ensembl ID: ENSOGAG00000004612
• Aliases: None
• Description: PIH1 domain containing 1 [Source:HGNC Symbol;Acc:26075]

Sequence

>retro_ogar_1564
CAGCCTGGTTTCTGCATAAAGACTAACTCATCGGAAGGGAAGGTTTTCATCAACATCTGTCACTCTGCCTCCATCCCTCC
TCCAGCTGACATGACTGAGGACGAGCTTCTTCAAATGCTGGAGGAGGACCAAGCTGGGTTTCACATCCTCATGAGTCTGA
GAGAGCCTCATGCTGAACTGGATGCAAAAGGCCAGGGCTGTACCGCCTACGATGTAGTTGTCAACAGCGACTTCTACAGG
AGGATGCTGAACAGCGATTTCTTGCGGGAGCTCGTGTCACCATTGCCAGGAAGGGCCTTAGATAAATAGAGCTTGCAGTT
GAATCCAGAATGGCGCATGTTGAAGAACCGGACTTTCCTGGGTTCCATCTCCCAGCAGAATATCAGCTCCCAGCCGCGTC
CTTGAATCCAGGAACTGGGAAATCTGTCCACGCCTGATTCCAGGAAAGATGAAGAAGGCCCTGAGAAGCCTCACCTGACT
CTCTGGATGGAAGCCCCTGACTCCTCTTGGCAGAAATTGACCTCCCCCAAACTGAATGACTGGGGCTGTCACTAGAGACT
GGGGAGAACCACCTGGTGATGAGGGGCCCCCAGCAGCTGTATCATCTAGATGTCTATATCCCCCTGCGGATCAACTCTGA
TGAGAGCAAGGCAACCTTCCACCGGAAGAGAAAACAATTGATGGTGACCATGCTCCTTCTGTCAGTGCCTTCC

Alignment

ORF - retro_ogar_1564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.14 %
• Parental protein coverage: 82.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPGFCIKTNSSEGKVFINICHSASIPPPADVTEDELLQMLEEDQAGFRIPMSLGEPHAELDAKGQGCTAY
          QPGFCIKTNSSEGKVFINICHSASIPPPAD.TEDELLQMLEEDQAGF.I.MSL.EPHAELDAKGQGCTAY
Retrocopy QPGFCIKTNSSEGKVFINICHSASIPPPADMTEDELLQMLEEDQAGFHILMSLREPHAELDAKGQGCTAY

Parental  DVAVNSDFYRRMQNSDFLRELVVTIAREGLEDKYSLQLNPEWRMLKNRTFLGSISQQNIRSQQRPRIQEL
          DV.VNSDFYRRM.NSDFLRELV.......L.DK.SLQLNPEWRMLKNRTFLGSISQQNI.SQ.RP.IQEL
Retrocopy DVVVNSDFYRRMLNSDFLRELVSPLPGRAL-DK*SLQLNPEWRMLKNRTFLGSISQQNISSQPRP*IQEL

Parental  GNLSMPDSRKDDEGPEKPHLTLWMEAPD-LLLAEIDLPKLNGALGLSLEIGENHLVMRGPQQLYHLDVYI
          GNLS.PDSRKD.EGPEKPHLTLWMEAPD.LLLAEIDLP.....LGLSLE.GENHLVMRGPQQLYHLDVYI
Retrocopy GNLSTPDSRKDEEGPEKPHLTLWMEAPD<LLLAEIDLPQTE-*LGLSLETGENHLVMRGPQQLYHLDVYI

Parental  PLRINSDESKAAFHQKRKQLMVAMPLLSVPS
          PLRINSDESKA.FH.KRKQLMV.M.LLSVPS
Retrocopy PLRINSDESKATFHRKRKQLMVTMLLLSVPS

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_1564 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000004612	2 retrocopies	retro_ogar_1564 , retro_ogar_2754,