RetrogeneDB ID: retro_ogar_2000

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873579.1:4435094..4435848(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VRK1
• Ensembl ID: ENSOGAG00000016785
• Aliases: None
• Description: vaccinia related kinase 1 [Source:HGNC Symbol;Acc:12718]

Sequence

>retro_ogar_2000
ATGCCTCGTGTAAAAGCAGCTCAAGCTGGAAGACAGGGCCCTGCAAAAAAACATCTTGCAGAACAGTTTGCAGCTGGGGA
GGTAGTAACTGACATGGGAATAAAAGAATAGAAAGTAGGATTACCCATTGGCCAAGGTGGCTTTGGCTGTATATATCTTG
CTGATACAAATTCTTCAAAATCAGTTGTCAGTGATGTACCCTGTGTTGTGAAAGTGGAACCCAGTGACAATGGACCTCTT
TTTACTGAATTAAAGTTCCACCAGCGAGCTGCTAAACCAAAGCAAATCCAGAAATGGATTCGTACCCATAAACTGAAGTA
CCTCGGTATTCCTAAGTATTGGGGGTCTGGTCTTCATGATAAAAATGGAAAAAGTTATAGGTTTATGATAATGGATCGCT
TTGGGAGTGACCTTCAGAAAATATATGAAGCAAATGCCAAAGGTTCTCTCGGAAAACTGTCTTGCAACTAGGCTTAAGAA
TTCTGGATATTCTTGAATATATTCATGAGCATGAGTACATACATGGAGATATCAAGACCTCAAATCTTCTTCTGAGCTAA
AGAATCCTGACCAGGTGTACTTGGTAGATTATGGCCTTGCCTATCGGTACTGCCCTGATGGAGTTCATAAAGAATACAAA
GAAGACCCCCAAAGATGTCATGATGGCACCATTGAATTCACCAGCATTGATGCACACAATGGCGTGGGCCCATCACGACG
TGGTGATTTGGAAATACGTGGTTATTGCATGATC

Alignment

ORF - retro_ogar_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.19 %
• Parental protein coverage: 70.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPRVKAAQAGRQGPAKRHLAEQFAAGEVVTDMGKKEWKVGLPIGQGGFGCIYLADTNSSKSVGSDAPCVV
          MPRVKAAQAGRQGPAK.HLAEQFAAGEVVTDMG.KE.KVGLPIGQGGFGCIYLADTNSSKSV.SD.PCVV
Retrocopy MPRVKAAQAGRQGPAKKHLAEQFAAGEVVTDMGIKE*KVGLPIGQGGFGCIYLADTNSSKSVVSDVPCVV

Parental  KVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTHKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQK
          KVEPSDNGPLFTELKF.QRAAKP.QIQKWIRTHKLKYLG.PKYWGSGLHDKNGKSYRFMIMDRFGSDLQK
Retrocopy KVEPSDNGPLFTELKFHQRAAKPKQIQKWIRTHKLKYLGIPKYWGSGLHDKNGKSYRFMIMDRFGSDLQK

Parental  IYEANAK-RFSRKSVLQLGLRILDVLEYIHEHEYVHGDIKASNLLLS-YKNPDQVYLVDYGLAYRYCPDG
          IYEANAK.RFSRK.VLQLGLRILD.LEYIHEHEY.HGDIK.SNLLLS..KNPDQVYLVDYGLAYRYCPDG
Retrocopy IYEANAK<RFSRKTVLQLGLRILDILEYIHEHEYIHGDIKTSNLLLS<LKNPDQVYLVDYGLAYRYCPDG

Parental  VHKEYKEDPKRCHDGTIEFTSIDAHNGVVVAPSRRGDLEILGYCMI
          VHKEYKEDP.RCHDGTIEFTSIDAHNG..V.PSRRGDLEI.GYCMI
Retrocopy VHKEYKEDPQRCHDGTIEFTSIDAHNG--VGPSRRGDLEIRGYCMI

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_2000 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000018006	1 retrocopy	retro_drer_17,
Macropus eugenii	ENSMEUG00000012543	1 retrocopy	retro_meug_186,
Otolemur garnettii	ENSOGAG00000003253	2 retrocopies	retro_ogar_1195, retro_ogar_825,
Otolemur garnettii	ENSOGAG00000008746	1 retrocopy	retro_ogar_1351,
Otolemur garnettii	ENSOGAG00000011587	1 retrocopy	retro_ogar_246,
Otolemur garnettii	ENSOGAG00000014866	1 retrocopy	retro_ogar_264,
Otolemur garnettii	ENSOGAG00000016063	1 retrocopy	retro_ogar_47,
Otolemur garnettii	ENSOGAG00000016785	1 retrocopy	retro_ogar_2000 ,
Ictidomys tridecemlineatus	ENSSTOG00000011492	1 retrocopy	retro_itri_1674,