RetrogeneDB ID: retro_ogar_1183

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873538.1:10751803..10752906(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSOGAG00000011440
• Aliases: None
• Description: ribosomal modification protein rimK-like family member B [Source:HGNC Symbol;Acc:29228]

Sequence

>retro_ogar_1183
ATGTGTAGCTCTGTGGCTGCCAAGCTGTGGTGTTTGATAGATTGTCGCATCAGGGAAGACTATCTCCAAAAAGAGATCTT
ATGAGCATTGAAGGCCAAATGCTGTGAGGAGGAACTAGACTTTAGGGCTGTGATGATGGATGAAGTGGTGCTGACAATAG
AACAAGGAAACCTAGGTCTTCGAGTCAATGGAGAACTAATCACCACCTACTCCCAAGTGGTGGTAGTGAGACTACCAACC
CCTTGAGTGTAAATTGATAGTGACATCACCGTTCTGCGTCATCTGGAGAAGATAGGGTGCCGGTTGAAGAACCGACCTCA
AGCTATCCTAAACTGTGTTAATAAGTTCTGGACATTTCAAGAGTTGGCTGGCCATGGCATTCCTCTGCTAGATACTTTCT
CTTATGGTAGCCATGAAAATTTTGCTAAGATGATTGATGAAGCAGAAGTACTGGAATTCCCAATGGTAGTGAAGAATACA
CAGGGTCATAGAGGCAAAGTTGTTTTCTTAGCTCGAGATAACCACCATTTGGCTGATCTAAGCCATCTTATTCAACATGA
AGCTCCATACCTATTCCAGAAGTATGTTGAAGAGTCTCACGGATGAGATGTCCATGTCATTGTTGTGAGAGGTTGTGTGG
TTGGCACCATGTTACGTTGTTCAACAGACGGGAGGATGCAAAGCAACTGCTCACTAGTGGTGTGGGGATGATGTGTTCAT
TGAGTGAACAAGGGAAACAGCTTGATATCCAGGAGTCTGATATCCTGGGGATGGATGTGCGTGGCATTGACCTATTGATG
AAAGATGACGGCTCCTTCCGTGTCTGTGAGGCCAATGCAAATGCAGGTTTCATCGCCTTTGATAAGGCTTGTAATCTAGA
CGTAGCTGGTATCATTGCGGACTATGCCGCCTGCCTTCTGCCCTCTAGCTGGCTCACCCAGCGTATGTCCCTGCTCTCTG
TGGTGTCCACGGCCAGTGAGACAAGTGAGCCAGAGCTGGGTCCCCCAGCCAGCACTGCTGTCGACAACATGAGCACAAGT
TCCAGCTCTGTCAACAGTGACCCTGAAAGCACAGAGCGAGAGATGCTCACCAAGCTTCTGGGT

Alignment

ORF - retro_ogar_1183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.62 %
• Parental protein coverage: 95.34 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCSSVAAKLWFLTDRRIREDYPQKEILRALKAKCCEEELDFRAVVMDEVVLTIEQGNLGLRINGELITAY
          MCSSVAAKLW.L.D.RIREDY.QKEIL.ALKAKCCEEELDFRAV.MDEVVLTIEQGNLGLR.NGELIT.Y
Retrocopy MCSSVAAKLWCLIDCRIREDYLQKEIL*ALKAKCCEEELDFRAVMMDEVVLTIEQGNLGLRVNGELITTY

Parental  PQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHEN
          .QVVVVR.PTP.V..DSDITVLRHLEK.GCRL.NRPQAILNCVNKFWTFQELAGHG.PL.DTFSYG.HEN
Retrocopy SQVVVVRLPTP*V*IDSDITVLRHLEKIGCRLKNRPQAILNCVNKFWTFQELAGHGIPLLDTFSYGSHEN

Parental  FAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYVKESHGRDVRVIVVG
          FAKMIDEAEVLEFPMVVKNT.GHRGK.VFLARD.HHLADLSHLI.HEAPYLFQKYV.ESHG.DV.VIVV.
Retrocopy FAKMIDEAEVLEFPMVVKNTQGHRGKVVFLARDNHHLADLSHLIQHEAPYLFQKYVEESHG*DVHVIVVR

Parental  GRVVGTMLRCSTDGRMQSNCSL-GGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFCVCEAN
          G.VVGTMLRCSTDGRMQSNCSL..GVGMMCSLSEQGKQL.IQ.S.ILGMDV.GIDLLMKDDGSF.VCEAN
Retrocopy GCVVGTMLRCSTDGRMQSNCSL<SGVGMMCSLSEQGKQLDIQESDILGMDVRGIDLLMKDDGSFRVCEAN

Parental  ANVGFIAFDKACNLDVAGIIADYAASLLPSGRLTRRMSLLSVVSTASETSEPELGPPASTAVDNMSASSS
          AN.GFIAFDKACNLDVAGIIADYAA.LLPS..LT.RMSLLSVVSTASETSEPELGPPASTAVDNMS.SSS
Retrocopy ANAGFIAFDKACNLDVAGIIADYAACLLPSSWLTQRMSLLSVVSTASETSEPELGPPASTAVDNMSTSSS

Parental  SVDSDPESTEREMLTKLPG
          SV.SDPESTEREMLTKL.G
Retrocopy SVNSDPESTEREMLTKLLG

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_1183 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
Homo sapiens	ENSG00000166532	1 retrocopy	retro_hsap_2506,
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31,
Oryctolagus cuniculus	ENSOCUG00000013997	1 retrocopy	retro_ocun_1777,
Otolemur garnettii	ENSOGAG00000000458	1 retrocopy	retro_ogar_3397,
Otolemur garnettii	ENSOGAG00000011440	2 retrocopies	retro_ogar_1183 , retro_ogar_2985,
Pongo abelii	ENSPPYG00000004244	1 retrocopy	retro_pabe_1844,
Pan troglodytes	ENSPTRG00000004643	1 retrocopy	retro_ptro_1457,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255,
Tarsius syrichta	ENSTSYG00000003996	1 retrocopy	retro_tsyr_1977,