RetrogeneDB ID: retro_tsyr_2160

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_97610:2689..4864(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT20H
• Ensembl ID: ENSTSYG00000013227
• Aliases: None
• Description: suppressor of Ty 20 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20596]

Sequence

>retro_tsyr_2160
ATGCAGCGAGCTTTGGATCGCGCAGAGCATATCATTCAAGGTGCCCGGCAGAGACCCCCTGAAAGGAAATACCGGTGGAG
TGGGGAAAAAACGCTACATCAAAAGCTGTATGACATTTATGTTGAAGAATGTGGAAGAGAGCCTGCGGGTATGCCGGAAC
TAAGGAGCAATGTAAATTTGTTGGAGAAGCTTGTTAGGAGAGAGCCGTTGCCCTGTTTAGTGGTCAGCCTGTACCCCGGC
AATGAGGAGTACTCGCTGATGCTCCGGGGGGAAAATGGATCCCCTTCCGAGATCATTCAACTGCCTTATGAAGAAAGGGA
GTTGCTCGAATACTTGTATGCAGAAGAACTACCTCCTGTTTTGGTTGACGTCCTGGACAAATCCCACATTAACATCTTTC
ACTGTGGGTGTGTCATCGCAGAAATACGCGACTACAGGCAGTCCAGGAAGAGGGGACCTCCCGGTTACCAAAGCAGGCAT
GTTCTCTTACGCCCCACGATGCAGACTTTAGTCCGTGATGTCCAGTCAATGACCAGGGATGGCCAGAAATGGACCCAGGA
AGACAGACTTCAGCTTGAGAGCCAACTGATCTTAGCTACAGCTGAGCCGCTGTGTCTGGATCCTTCTGTAGCAGTCACCT
GCACTACCAACAGGCTGCTGTACAACAAGCAAAAGATGAACACCGGCCCGATGAAACGGCACTTCAAGAGGTACGCGTGG
CCCTCTCTCAGTCAGCAGCAGGAGCCGTCTGGTCGTCCACCTCCACCTGAGCTAAGAGTTTTGACTTCTGGCAAAAAAGG
CAAAGGAAGAAAAGCAGGTCAGCATCATGACCTGAAAATTTCTAAAGCCGGAAACTGTGTAGAAACGTGGAAACGGAGAC
CCTGCGACTTGGCCACACCTTCTCAAGTGGATGTGGAGAAAGATGCTAAAGGGAAACGGTCTGTCAGATCTCATCACTCA
CGACCAACCGTCTGGCCAGCCCGGGGGGTACAAGATGATTGTGGATCCCAACGTGAGGCTGGCGGCCAGTCCCGGGCAGC
AAAGCCGAGCACCGTGCAGTCCCTTCGCGACCCACTTATCTCTGGTCAAACATGGCCATCGAAAAAAGCCACGTGGAAGA
GTCCGAAGTCTCCCCTCCCCTCCTTCCTAGATGACCACTCATATGTTCTCAGGCCTGGGTCAGAGACAGATGCCAGGAGG
GCAGTCAGACAGCACCGGGAATCGGTGCAGGGCAAAGCCAGAGGTCCAGGCAAGATGTCACACAGCTCCAGCCGCCCAGC
CAGTGGCAGTCAGCTCTCTTCAGCGGAAACACCGGAACCGCCTAAACCCACGTCGGTCCAGTCTTCAGTACCGGGGAAGG
AGGTGAAACATCCCCCTCCAGCCATCCTACTTTCCTCAAGCTCAGGAAAGAGCTCTTCTGGTAACACTTTTCCTCCACAG
CAGGCAAGCAGCTCTCTTCCATCTCCATCCCCTGCTGGTGCTCATGCTCCTGCAGCAGCAAGTCTTTCTCGGAAGTCCTC
CGTCGATCTCAAGCCAGTTAGCGGGCTTCTTCCCGCTGTCCAGTCCCCTGCCAGCTCCTCAAAAACAACCCCAGCCACCC
ATGTCACGGCTTGGCCAGGTGCCACTGGCCTCGAGGTCATCAGTGTGAAGGGCCCGGTCCTCGGGGCTCAGACTCTGGGG
AGTGGTTCAAACCCCGTGTGGGGCCAGACCACCGGTGCCCTGGCACCTACCCACGTCAGTGCAGGCAGCCCTCGGTTCTC
AGGAGGTCCACTACCAAACGCACAGCCCGGTGCAGTGCAGGCACCTTCTCAAGCTCACGTCCAGTATTTTTTAAAAGCTC
CCTCAGGTCTCAAGCCCTTGACTCTACTCCAGGTTCCACCTGGTTCCCTCATTTTGGCCACCGAGCAGCAGCAGTTGTAC
CAGTTGGGTCCGTGGCAAGGCCTCCAGCAACACACAGTTTTGCATCCTCTTCAGCCGGGGCTTCAGGGTTCTGCACGGGT
TTCGAGCAGTCGAGAACGGGCCTTACCTGCTCATCGCCCTCTTCTTGTTAATCTCACTGGAGCTAGGAGTGGTCTCCAGC
CCCAGGCAGCTGTGTTGTCTCAGCCTGACTCTGAGAAGAGAAGAGCTGGGCAGAGCCTACCTCAGCAGGGATCTCAGCTC
CCCTCTACCTTGCGG

Alignment

ORF - retro_tsyr_2160 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.93 %
• Parental protein coverage: 92.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LELALDRAEYVIESARQRP-KRKYLSSGRKSVFQKLYDLYIEECEKEPE-VKKLRRNVNLLEKLVMQETL
          ...ALDRAE..I..ARQRP..RKY..SG.K...QKLYD.Y.EEC..EP.....LR.NVNLLEKLV..E.L
Retrocopy MQRALDRAEHIIQGARQRPPERKYRWSGEKTLHQKLYDIYVEECGREPAGMPELRSNVNLLEKLVRREPL

Parental  SCLVVNLYPGNEG-SLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCGCVIA
          .CLVV.LYPGNE..SLMLRG.NGS.SE.I.LPYEE.ELLEYL.AEELPP.LVD.L.KS..NIFHCGCVIA
Retrocopy PCLVVSLYPGNEEYSLMLRGENGSPSEIIQLPYEERELLEYLYAEELPPVLVDVLDKSHINIFHCGCVIA

Parental  EIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCLDPSI
          EIRDYRQS.....PGYQSRH.LLRPTMQTL..DV.S.T.D..KWTQED.L.LESQLILATAEPLCLDPS.
Retrocopy EIRDYRQSRKRGPPGYQSRHVLLRPTMQTLVRDVQSMTRDGQKWTQEDRLQLESQLILATAEPLCLDPSV

Parental  AVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSHCPPPPQLKLLDFLQKRKERKAGQHYDLKI
          AVTCT.NRLLYNKQKMNT.PMKR.FKRY...SL..QQ..S..PPPP.L..L....K.K.RKAGQH.DLKI
Retrocopy AVTCTTNRLLYNKQKMNTGPMKRHFKRYAWPSLSQQQEPSGRPPPPELRVLTSGKKGKGRKAGQHHDLKI

Parental  SKAGNCVDMWKRSPCNLAIPSEVDVEKYAKVEKSIKSDDSQPAVWPAHDVKDDYVFECEAGTQYQKTKLT
          SKAGNCV..WKR.PC.LA.PS.VDVEK.AK...S..S..S.P.VWPA..V.DD.....EAG.Q....K..
Retrocopy SKAGNCVETWKRRPCDLATPSQVDVEKDAKGKRSVRSHHSRPTVWPARGVQDDCGSQREAGGQSRAAKPS

Parental  ILQSLGDPLYYGKIQPCKAEEENDNQMSPSHFSTDDHSNWFVIGSKTDAERVVNQYQELVQNEAKCPVKM
          ..QSL.DPL..G...P.K.........SP.....DDHS.....GS.TDA.R.V.Q..E.VQ..A..P.KM
Retrocopy TVQSLRDPLISGQTWPSK-KATWKSPKSPLPSFLDDHSYVLRPGSETDARRAVRQHRESVQGKARGPGKM

Parental  SHSSSGSASLSQLSPGKEAEQPETVSVQSSVLGKGVKHRPPPIKLPSSSGNSSSGNYFTPQQASSFLKSP
          SHSSS..AS.SQLS.....E.P...SVQSSV.GK.VKH.PP.I.L.SSSG.SSSGN.F.PQQASS.L.SP
Retrocopy SHSSSRPASGSQLSSAETPEPPKPTSVQSSVPGKEVKHPPPAILLSSSSGKSSSGNTFPPQQASSSLPSP

Parental  TPPPSSKP--PSLSRKSSVDLNQVGMLSPAALSPASSSQRNTATQVMA--NSTGLNFINVVGSVCGAQAL
          .P.....P...SLSRKSSVDL..V..L.PA..SPASSS....AT.V.A....TGL..I.V.G.V.GAQ.L
Retrocopy SPAGAHAPAAASLSRKSSVDLKPVSGLLPAVQSPASSSKTTPATHVTAWPGATGLEVISVKGPVLGAQTL

Parental  MSGSNPMLSCNTGAITPAGINLSSLLPSGGLLPNALPSAMPAASQAGVPFGLKNTSSLRPLNLLQLPGGS
          .SGSNP.....TGA..P......S...SGG.LPNA.P.A..A.SQA.V...LK..S.L.PL.LLQ.P.GS
Retrocopy GSGSNPVWGQTTGALAPTHVSAGSPRFSGGPLPNAQPGAVQAPSQAHVQYFLKAPSGLKPLTLLQVPPGS

Parental  LIFNTLQQQQQQLSQFTPQQPQQPTTSSPQQPGEQXXXXXXXXXXXXXXXXQAAVINLTGVGSFMQSQAA
          LI..T.QQQ..QL.....Q..QQ.T...P.QPG.Q.....................NLTG..S..Q.QAA
Retrocopy LILATEQQQLYQLGPW--QGLQQHTVLHPLQPGLQGSARVSSSRERALPAHRPLLVNLTGARSGLQPQAA

Parental  VLSQLGSAENRPEQSLPQQRFQLSSAFQ
          VLSQ..S...R..QSLPQQ..QL.S...
Retrocopy VLSQPDSEKRRAGQSLPQQGSQLPSTLR

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_2160 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000116	2 retrocopies	retro_ecab_1052, retro_ecab_1101,
Homo sapiens	ENSG00000102710	2 retrocopies	retro_hsap_4659, retro_hsap_4794,
Loxodonta africana	ENSLAFG00000027507	1 retrocopy	retro_lafr_1199,
Macaca mulatta	ENSMMUG00000003590	2 retrocopies	retro_mmul_2479, retro_mmul_2555,
Pongo abelii	ENSPPYG00000005288	2 retrocopies	retro_pabe_3619, retro_pabe_3729,
Pan troglodytes	ENSPTRG00000005791	2 retrocopies	retro_ptro_3095, retro_ptro_3189,
Pteropus vampyrus	ENSPVAG00000014609	1 retrocopy	retro_pvam_401,
Tarsius syrichta	ENSTSYG00000013227	1 retrocopy	retro_tsyr_2160 ,
Vicugna pacos	ENSVPAG00000007288	1 retrocopy	retro_vpac_193,