RetrogeneDB ID: retro_tsyr_1977

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_74304:2416..3353(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSTSYG00000003996
• Aliases: None
• Description: ribosomal modification protein rimK-like family member B [Source:HGNC Symbol;Acc:29228]

Sequence

>retro_tsyr_1977
ATATGTCGCTCTGTGGCTGTCAAGTTGTGGTTTTGGACAGATGGTCACATCAGGGAAGACTATTCCCCAAAAAAGATCTT
ACGAGCATTGAAAGACAAGTGCTGTGAGGAGGAACTGGACTTCAGAGCTGTGGTGGTGGATGAGGTGGTGCTGACAACGA
GCAGGAAAACCTGGGCCTCCAGAACAATGGAGAACTAATCAATGCATACCGCCAAGCGGTGGTAGTGAGAGTACCAACCC
CTTGGGTGCAAAGTGATAGTGACATCACTGTTTTGCACCATCTAGAGAAGATGGGATGAAAATTGATGAGCTGACCTCAA
GCCATCTTGAACTGTGTTAATAAGTCCTGGACATTTCAAGAGTTGACTGGCCATGGTGATCCTCTGCTAGATATTTTCTT
TTATGGTGGCTGTGAAAACTTTGTTAAAATGATTGATGAAGCAGAAGCACTGGAATTCCCAATGGTAGTGAAGAATACAC
TGGGCCATAGAGATAAAGCTGTTTGCTTGGCTCGAGATAAGCATCATTTGACTGATCCAAGCCATCTTACTCACCATGAA
GCTCTGTACCTGTTCCAGAAATATGTTAAGGAGTCTCATGGACAGGATGTATGTGTTACTGTCATGAAAGCCCATGTGGT
TGCCACCATGTTACCTTGTTCAACAGACAGGAGAATGCAAAGCAACTGCTCACTAGGTGGTGTGGGAATGGTGTGCTCAT
TGAGTGAACAGGGAAATAACTGGCTATCCAGGTGTCTAATATCCTGGGGATGGATGTGTGTGGCACTGACCTGTTGATGA
AAGATGGTAGCTTCTTCTGTGTCTTCAAGGCCAGTGCAAATGTAGGTATCATCGTCTTTGATAAGGATTGTAATCTAGAT
GTAGGTGGTGTCACAGCGGACTGTGCTGTCTCCCTTCTACTCTCTGGCTGACTCACC

Alignment

ORF - retro_tsyr_1977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.46 %
• Parental protein coverage: 81.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCSSVAAKLWFLTDRRIREDYPQKEILRALKAKCCEEELDFRAVVMDEVVLTI-EQGNLGLRINGELITT
          .C.SVA.KLWF.TD..IREDY..K.ILRALK.KCCEEELDFRAVV.DEVVLT..EQ.NLGL..NGELI..
Retrocopy ICRSVAVKLWFWTDGHIREDYSPKKILRALKDKCCEEELDFRAVVVDEVVLTT<EQENLGLQNNGELINA

Parental  YPQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHE
          Y.Q.VVVRVPTPWVQSDSDITVL.HLEKMG..LM..PQAILNCVNK.WTFQEL.GHG.PL.D.F.YGG.E
Retrocopy YRQAVVVRVPTPWVQSDSDITVLHHLEKMG*KLMS*PQAILNCVNKSWTFQELTGHGDPLLDIFFYGGCE

Parental  NFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYVKESHGRDVRVIVV
          NF.KMIDEAE.LEFPMVVKNT.GHR.KAV.LARDKHHL.D.SHL..HEA.YLFQKYVKESHG.DV.V.V.
Retrocopy NFVKMIDEAEALEFPMVVKNTLGHRDKAVCLARDKHHLTDPSHLTHHEALYLFQKYVKESHGQDVCVTVM

Parental  GGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQ-GKQLAIQVSNILGMDVCGIDLLMKDDGSFCVCEA
          ...VV.TML.CSTD.RMQSNCSLGGVGM.CSLSEQ.GK.LAIQVSNILGMDVCG.DLLMKD...FCV..A
Retrocopy KAHVVATMLPCSTDRRMQSNCSLGGVGMVCSLSEQ<GK*LAIQVSNILGMDVCGTDLLMKDGSFFCVFKA

Parental  NANVGFIAFDKACNLDVAGVIADYAASLLPSGRLT
          .ANVG.I.FDK.CNLDV.GV.AD.A.SLL.SG.LT
Retrocopy SANVGIIVFDKDCNLDVGGVTADCAVSLLLSG*LT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1977 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 8 parental genes, and 9 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	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 ,