RetrogeneDB ID: retro_ogar_509

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873522.1:17220884..17221776(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDK1
• Ensembl ID: ENSOGAG00000014761
• Aliases: None
• Description: pyruvate dehydrogenase kinase, isozyme 1 [Source:HGNC Symbol;Acc:8809]

Sequence

>retro_ogar_509
GTGAGGCTGGCGCGGCTGCTGCGCGGGGCCGGCCCGGGCCCGGGGCCGTTCGCCTCCGGCCCCCGCTCCGGCCGCAGCCT
CAGCTCGGACTCGGGCTCCGGCCCGGCGCCCGCAAGTGGCGTTCCCGGCCAGGTGGACTTCTACGCGCGCTTCTCGCCGT
CCCCGCTCTCCATGAAGCAGTTCCTGGACTTCGGATCGGTGAACGCTTGCGAAAAGACCTCATTTATATTTCTGCGGCAA
GAGTTGCCCGTTAGATTGGCAAATATAATGAAAGAAATAAGTCTTCTCCCAGACAATCTTCTCAGGACGCCATCCGTTCA
GTGGGTACAAAGCTGGTATATCCAGAGTCTTCAGGAGCTTCTTGATTTTAAGGACAGAAGTGCTGAGGATGCTAAAGCCG
TATGTGACTTTACAGATACGTGATACGGATCCGAAACCGACACAGTGATGTCATTCCCACCATGGCCCAGGGTGTGATTG
AATACCAGGAGAGCTTCGGGTGGATCCTGTCACCAGCCAGAATGTTCAGTACTTTCTGGATCGATTCTACATGAGTCGCA
TTTCAATTAGAATGTTACTCTATCAGCACTCTCTATTATTTGGTGGAAAAGGCAAAGGAAATCCCTCTCATCAAAGACAC
ATTGGAAGCATAAACCCAAACTGCAATGTAGTGGAAGTTATTAAAGATGGCTATGAGAATGGTAGGCGTCTTTGTGATTT
GTATTATATTATCTCCCCTGAACTAGAACTTGGAGAACTAAATGCAAAATCACCAAGACAGCCAATACAAGTGGTTTATG
TACCATCCCATCTCTATCACATGGTGTTTGAACTTTTCAAGAACGCAATGAGAGCAACCATGGAACACCAGGCAGACAAA
GCTGTTTACCCC

Alignment

ORF - retro_ogar_509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95. %
• Parental protein coverage: 68.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRLARLLRGAGSGPGPFASGPRSGRSLSSDSGSGPAPASGVPGQVDFYARFSPSPLSMKQFLDFGSVNAC
          .RLARLLRGAG.GPGPFASGPRSGRSLSSDSGSGPAPASGVPGQVDFYARFSPSPLSMKQFLDFGSVNAC
Retrocopy VRLARLLRGAGPGPGPFASGPRSGRSLSSDSGSGPAPASGVPGQVDFYARFSPSPLSMKQFLDFGSVNAC

Parental  EKTSFMFLRQELPVRLANIMKEISLLPDNLLRTPSVQLVQSWYIQSLQELLDFKDRSAEDAKAVYDFTDT
          EKTSF.FLRQELPVRLANIMKEISLLPDNLLRTPSVQ.VQSWYIQSLQELLDFKDRSAEDAKAV.DFTDT
Retrocopy EKTSFIFLRQELPVRLANIMKEISLLPDNLLRTPSVQWVQSWYIQSLQELLDFKDRSAEDAKAVCDFTDT

Parental  -VIRIRNRHNDVIPTMAQGVIEYKESFG-VDPVTSQNVQYFLDRFYMSRISIRMLLNQHSLLFGGKGKGN
          .VIRIRNRH.DVIPTMAQGVIEY.ESFG.VDPVTSQNVQYFLDRFYMSRISIRMLL.QHSLLFGGKGKGN
Retrocopy <VIRIRNRHSDVIPTMAQGVIEYQESFG<VDPVTSQNVQYFLDRFYMSRISIRMLLYQHSLLFGGKGKGN

Parental  PSHQRHIGSINPNCNVVEVIKDGYENARRLCDLYYINSPELELGELNAKSPGQPIQVVYVPSHLYHMVFE
          PSHQRHIGSINPNCNVVEVIKDGYEN.RRLCDLYYI.SPELELGELNAKSP.QPIQVVYVPSHLYHMVFE
Retrocopy PSHQRHIGSINPNCNVVEVIKDGYENGRRLCDLYYIISPELELGELNAKSPRQPIQVVYVPSHLYHMVFE

Parental  LFKNAMRATMEHHADKGVYP
          LFKNAMRATMEH.ADK.VYP
Retrocopy LFKNAMRATMEHQADKAVYP

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_509 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007507	1 retrocopy	retro_cjac_4090,
Cavia porcellus	ENSCPOG00000008434	1 retrocopy	retro_cpor_545,
Macaca mulatta	ENSMMUG00000022553	1 retrocopy	retro_mmul_2511,
Monodelphis domestica	ENSMODG00000009035	2 retrocopies	retro_mdom_107, retro_mdom_1447,
Otolemur garnettii	ENSOGAG00000005598	2 retrocopies	retro_ogar_1213, retro_ogar_1980,
Otolemur garnettii	ENSOGAG00000014761	1 retrocopy	retro_ogar_509 ,