RetrogeneDB ID: retro_ogar_2985

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873693.1:1304584..1305433(+)
• 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_2985
ATGTGTAGCTCTGTGGCTGCCAAGTTGTGGTTTTTGACAGATCGTTGCATCAGGGAAGACTATCCCCAAAAAGAGATCTT
ACGAGCGTGGAAGGCCAAATGCTGTGATGAGAAACTGGACTTTAGGGCTGTGGCGCTGGATGAAGTGGTGCTGACAATAG
AGCAAGGAAACCTAGGTCTTCGAATCAATGGAGAACTAATCACTGTCTACCCCCAAGTGGTGGTGGTGAGAGTACCAACC
CCTTGGGTGCAAAGTGATAGTGACATCACCATTCTGCGCCATCTGGAGAAGATGGGGTGCCAGTTGATGAACTGACTTCA
AGCTATCCTGAACTGTGTTAATAAGTTCTGGACATTTCAAGAGTTGAGTGCCCACGGTGTTCCTCTGCCAAGATACTTTC
CCTTATGGTGGCCATGAACATTTTGCTAAAATGATTGATGAAGCAGAAGTACTGGAATTCCCAATGGTAGCGAAGAATAC
ACAGGGTCAGAGGCAAAGCTGTTTTCTTAGCTTGAAGTAAGCACCATTTGGCTGATCTAAGCCATCTTCTTCGACATGAA
GCTCAATACCTATTCCAGAAGTATGTTGAAGAGTCTCCCGGACCAGATGTCCGTGTCATTGTTGTGGGAGGTCGTTGGTT
GGCACCATTTACACTGTTCAACAGATGCAAAGCAACTGCTCACTAGTGGTGTGGGGATGACGTGCTCATTGAGTGAACAA
GGGGAAAAGTTCGCTGTCCAGGAGTCTGATATCCTGGGGATGGATGTGCGTGGCATTGACCTATTGATGAAAGATGACAG
CTCCTTCTGTGTCTTCGAGGCCAATGCAAATGCAGGTTTCATCGCCTTT

Alignment

ORF - retro_ogar_2985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.73 %
• Parental protein coverage: 74.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MCSSVAAKLWFLTDRRIREDYPQKEILRALKAKCCEEELDFRAVVMDEVVLTIEQGNLGLRINGELITAY
          MCSSVAAKLWFLTDR.IREDYPQKEILRA.KAKCC.E.LDFRAV..DEVVLTIEQGNLGLRINGELIT.Y
Retrocopy MCSSVAAKLWFLTDRCIREDYPQKEILRAWKAKCCDEKLDFRAVALDEVVLTIEQGNLGLRINGELITVY

Parental  PQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLP-DTFSYGGHE
          PQVVVVRVPTPWVQSDSDIT.LRHLEKMGC.LMN..QAILNCVNKFWTFQEL..HGVPLP.DTF.YGGHE
Retrocopy PQVVVVRVPTPWVQSDSDITILRHLEKMGCQLMN*LQAILNCVNKFWTFQELSAHGVPLP>DTFPYGGHE

Parental  NFAKMIDEAEVLEFPMVVKNTRGHRGKAVFL-ARDKHHLADLSHLIRHEAPYLFQKYVKESHGRDVRVIV
          .FAKMIDEAEVLEFPMV.KNT.G.R....FL.A..KHHLADLSHL.RHEA.YLFQKYV.ES.G.DVRVIV
Retrocopy HFAKMIDEAEVLEFPMVAKNTQGQR-QSCFL>A*SKHHLADLSHLLRHEAQYLFQKYVEESPGPDVRVIV

Parental  VGGR-VVGTM-LRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFCVC
          VGGR..VGT..L.CSTD.........G...M.CSLSEQG...A.Q.S.ILGMDV.GIDLLMKDD.SFCV.
Retrocopy VGGR<LVGTI<LHCSTDAKQLLTSGVG---MTCSLSEQGEKFAVQESDILGMDVRGIDLLMKDDSSFCVF

Parental  EANANVGFIAF
          EANAN.GFIAF
Retrocopy EANANAGFIAF

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_2985 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,