RetrogeneDB ID: retro_ogar_913

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:31741677..31742834(+)
• Located in intron of: ENSOGAG00000011648

Retrocopy information

• Ensembl ID: ENSOGAG00000034839
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VPS36
• Ensembl ID: ENSOGAG00000011312
• Aliases: None
• Description: vacuolar protein sorting 36 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20312]

Sequence

>retro_ogar_913
ATGGACCGCTTGTGTGGACCAGCGGCCTCTTGGAAATCAACGAGACTCTAGTGATCCAACAGCGCGGGGTGCGCATCTAC
GACGGCGAGGAGAAGATCAAATTTGATGCTGGGACACTCCTTCTTAGTACACATCATCTGATTTGGAGAGATCATAAAAA
TCATGAGTGCTGCATGGCCATTCCTCTTTCCCAAATTGTGTTCATTGAAGAACAGGCAGCTGGAATTGGGAAGAGTGCCA
AAATAGTGGTTCATCTTCACACAGCTCCTCCTAACAAAGAACCTGGACCATTCCAGAGGAGTAAGAACTCCTACATCAAA
CTGTCTTTCAGAGAACATGGTCAGATTGAGTTTTATAGGCGTTTATCAGAGGAAATGACACAGAGAAGATGGGAGAATGT
ACCAGTTTCCCAGTCATTACAAACAAGTAGAGGACCCCAGCCAGGAAGAATAAGAGCTGTAGGAATTGTAGGTATTGAAA
GGAAACTGGAAGAAAAAAGAAAAGAAACAGACAAAAACATTTCTGAGGCTTTTGAAGACCTCAGCAAGTTAATGATCAAG
GCTAAAGAAATGGTGGAATTATCAAAATCAATTGCTAATAAAATTAAAGAAAAACAAGGAGACATCACAGAAGATGAGAC
CATCAGGTTTAAATCCTACTTGCTGAGCATGGGAATAGCTAACCCAGTGACCAGGGAAACCTACGGCTCCGGCACACAGT
ACCACATGCAGCTGGCCAAACAGCTGGCTGGGATATTGCAGGTGCCTTTACAGGAACGAGGGGGAATCATGTCACTGACG
GAGGTATACTGTTTAGTAAACCGCGCTCGAGGAATGGAATTGCTCTCACCAGAAGATTTAGTAAATGCGTGCAAAATGCT
GGAAGCACTGAAATTACCTCTCAGGCTCCAAGTTTTTGACAGCGGTGTCATGGTAATCGAGCTGCAGTCCCACAAGGAAG
AGGAAATGGTGGCCTCGGCCCTGGAGACAGTTTCAGAAAAGGGATCTCTAACATCAGAAGAGTTTGCTAAGCTTGTGGGA
ATGTCTGTCCTCCTGGCCAAAGAAAGGTTGCTGCTTGCAGAGAAGATGGGACATCTTTGCCGAGATGACTCAGTGGAAGG
CTTGCGTTTTTACCCAAATTTATTTATGACACAGAGC

Alignment

ORF - retro_ogar_913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDRF-VWTSGLLEINETLVIQQRGVRIYDGEEKIKFDAGTLLLSTHRLIWRDHKNHECCMAIPLSQIVFI
          MDR..VWTSGLLEINETLVIQQRGVRIYDGEEKIKFDAGTLLLSTH.LIWRDHKNHECCMAIPLSQIVFI
Retrocopy MDRL<VWTSGLLEINETLVIQQRGVRIYDGEEKIKFDAGTLLLSTHHLIWRDHKNHECCMAIPLSQIVFI

Parental  EEQAAGIGKSAKIVVHLHTAPPNKEPGPFQRSKNSYIKLSFREHGQIEFYRRLSEEMTQRRWENVPVSQS
          EEQAAGIGKSAKIVVHLHTAPPNKEPGPFQRSKNSYIKLSFREHGQIEFYRRLSEEMTQRRWENVPVSQS
Retrocopy EEQAAGIGKSAKIVVHLHTAPPNKEPGPFQRSKNSYIKLSFREHGQIEFYRRLSEEMTQRRWENVPVSQS

Parental  LQTSRGPQPGRIRAVGIVGIERKLEEKRKETDKNISEAFEDLSKLMIKAKEMVELSKSIANKIKEKQGDI
          LQTSRGPQPGRIRAVGIVGIERK...........ISEAFEDLSKLMIKAKEMVELSKSIANKIKEKQGDI
Retrocopy LQTSRGPQPGRIRAVGIVGIERKXXXXXXXXXXXISEAFEDLSKLMIKAKEMVELSKSIANKIKEKQGDI

Parental  TEDETIRFKSYLLSMGIANPVTRETYGSGTQYHMQLAKQLAGILQVPLQERGGIMSLTEVYCLVNRARGM
          TEDETIRFKSYLLSMGIANPVTRETYGSGTQYHMQLAKQLAGILQVPLQERGGIMSLTEVYCLVNRARGM
Retrocopy TEDETIRFKSYLLSMGIANPVTRETYGSGTQYHMQLAKQLAGILQVPLQERGGIMSLTEVYCLVNRARGM

Parental  ELLSPEDLVNACKMLEALKLPLRLRVFDSGVMVIELQSHKEEEMVASALETVSEKGSLTSEEFAKLVGMS
          ELLSPEDLVNACKMLEALKLPLRL.VFDSGVMVIELQSHKEEEMVASALETVSEKGSLTSEEFAKLVGMS
Retrocopy ELLSPEDLVNACKMLEALKLPLRLQVFDSGVMVIELQSHKEEEMVASALETVSEKGSLTSEEFAKLVGMS

Parental  VLLAKERLLLAEKMGHLCRDDSVEGLRFYPNLFMTQS
          VLLAKERLLLAEKMGHLCRDDSVEGLRFYPNLFMTQS
Retrocopy VLLAKERLLLAEKMGHLCRDDSVEGLRFYPNLFMTQS

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_913 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008949	1 retrocopy	retro_chof_702,
Macaca mulatta	ENSMMUG00000011360	1 retrocopy	retro_mmul_2510,
Otolemur garnettii	ENSOGAG00000011312	1 retrocopy	retro_ogar_913 ,
Ictidomys tridecemlineatus	ENSSTOG00000004651	1 retrocopy	retro_itri_97,