RetrogeneDB ID: retro_tsyr_1547

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_48549:1314..2732(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA3
• Ensembl ID: ENSTSYG00000008134
• Aliases: None
• Description: karyopherin alpha 3 (importin alpha 4) [Source:HGNC Symbol;Acc:6396]

Sequence

>retro_tsyr_1547
ACGATGCAAAGGCACAGAAATGAAGCTGAACTGTGGAAGAGCAAAAGGGATGAACACTTATTGAAAAAGAGAAATGTTCC
CCAAGAAGAAAGTTTAGAAGATTCAGATGTTAATGCTGATTTTAAAGCACAAAATGTAACACTAGAAGCTATATTGCAGA
ATGCCACAAATGATAACCCAGGGGTCCAGTTGGGTGCTGTGCAGGCAGCAAGAAAACTACTATCTAGTGAGAGAAACCCA
CCAATTGATGACCTAATAAAGTCTGGGATTTTACCAATTCTAGCCAAATGTCTAGAAAGGGATGATAATCCTTCATTACA
GTTTGAAGCTGCTTGGGCATTAAATAATACAGCATCAGGAACTTCTGCACAGACTCAAGCTATTGTACAATCTAATGCAG
TACCTCTTTTTCTGAGACTTCTTCATTCACCACATCAAAATGTTTGTGAACAAACAGTGTGGGCATTGGGAAACATTATA
GGTGATGGTCCTCAATGTAGAGATTATGTCATATCACTGGGAGTTGTCAAACCTCTTCCGTCCTTCATCAGTCCCTCCAT
TTCCAACACCTTCCTTGGGAAAGTCACATGGGTCATTGTCAATCTCAGCAGGAATAAGGATCCCCCACCGTCTATGGAGA
CAGTTCAGGAGATTTGGGCAGCTTTATGTGTCCTCATATACCATACAGACATAAACATTCTTGTAGACACTGTTTGGGCT
CTGCCATACTTGACAGATGAGCAGATAAAGATGGTTATTGATTCAGGGGTTGTGCCATTTCTCGTGCCCTCTCTGAGTCA
CCAGGAAGTGAAAGTTCAAACAGCTGCACTCAGAGCAGTAGGCAACATAGTGACTGCCACTGATGAGCAGACCCAGGTTG
TTCTCAATTGTGACGTCCTGTCACACTTCCCAAATATTTTATCACACCCAAAAAAGAAGATAAATAAGGAAGCAGTATGG
TTCCTTTCCAACATAACAGCAGGCAAACCAGCAACAAGTTCAAGCAGTAATAGATGCTGGATTAATCCCTATGATTATTC
ATCAGCTAACTAAGGGAGGTTTGGGAACACAAAAGGAAACTGCTTGGACAATCAGCAATTTAACAATAAATGGCAGAAAG
GATCAGATTGAGTACCTTGTACAGCAGAATGTAATACCACCGTTTTATAATTTACTGTCAGTGAAAGATTCTCAAGTGGT
TCCAGATGGCCTAAAAAAGCATTCCAATAATGACTGGTGATGAAGCAAGCACGATAGCTGAAATAATAGAGGAATGTGGA
GGTTTAGAGAAAATTGAAGTTTTGCAGCAACATGAAAATGAAGACATATATAAATTAGCATTTGGAATCATAGATCAGTA
TTTCTCTGATGATGATATCGATGAAGATCCCAACCTCATTCCTGAAGCAACATAGGGA

Alignment

ORF - retro_tsyr_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 96.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TMRRHRNEVTVELRKNKRDEHLLKKRNVPQEESLEDSDVDADFKAQNVTLEAILQNATSDNPVVQLSAVQ
          TM.RHRNE...EL.K.KRDEHLLKKRNVPQEESLEDSDV.ADFKAQNVTLEAILQNAT.DNP.VQL.AVQ
Retrocopy TMQRHRNEA--ELWKSKRDEHLLKKRNVPQEESLEDSDVNADFKAQNVTLEAILQNATNDNPGVQLGAVQ

Parental  AARKLLSSDRNPPIDDL-KSGIL-ILVKXXXXXXXPSLQFEAAWALTNIASGTSAQTQAVVQSNAVPLFL
          AARKLLSS.RNPPIDDL.KSGIL.IL.K.......PSLQFEAAWAL.N.ASGTSAQTQA.VQSNAVPLFL
Retrocopy AARKLLSSERNPPIDDLIKSGILPILAKCLERDDNPSLQFEAAWALNNTASGTSAQTQAIVQSNAVPLFL

Parental  RLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFINPSIPITFLRNVTWVIVNLCRNKDP
          RLLHSPHQNVCEQ.VWALGNIIGDGPQCRDYVISLGVVKPL.SFI.PSI..TFL..VTWVIVNL.RNKDP
Retrocopy RLLHSPHQNVCEQTVWALGNIIGDGPQCRDYVISLGVVKPLPSFISPSISNTFLGKVTWVIVNLSRNKDP

Parental  PPPMETVQEILPALCVLIYHTDINILVDTVWALSYLTDGGNEQIQMVIDSGVVPFLVPLLSHQEVKVQTA
          PP.METVQEI..ALCVLIYHTDINILVDTVWAL.YLTD...EQI.MVIDSGVVPFLVP.LSHQEVKVQTA
Retrocopy PPSMETVQEIWAALCVLIYHTDINILVDTVWALPYLTD---EQIKMVIDSGVVPFLVPSLSHQEVKVQTA

Parental  ALRAVGNIVTGTDEQTQVVLNCDVLSHFPNLLSHPKEKINKEAVWFLSNITA-RNQQQVQAV-DAGL-PM
          ALRAVGNIVT.TDEQTQVVLNCDVLSHFPN.LSHPK.KINKEAVWFLSNITA..NQQQVQAV.DAGL.PM
Retrocopy ALRAVGNIVTATDEQTQVVLNCDVLSHFPNILSHPKKKINKEAVWFLSNITA>ANQQQVQAVIDAGLIPM

Parental  IIHQLANGDFGTQKEAAWAISNLTISGRKDQVEYLVQQNVIPPFCNLLSVKDSQVVQVVLDGL-KNILIM
          IIHQL..G..GTQKE.AW.ISNLTI.GRKDQ.EYLVQQNVIPPF.NLLSVKDSQVV....DGL.K.I.IM
Retrocopy IIHQLTKGGLGTQKETAWTISNLTINGRKDQIEYLVQQNVIPPFYNLLSVKDSQVVP---DGL>KSIPIM

Parental  AGDEASTIAEIIEECGGLEKIDVLQQHENEDIYKLAFEIIDQYFSGDDIDEDPSLIPEATQG
          .GDEASTIAEIIEECGGLEKI.VLQQHENEDIYKLAF.IIDQYFS.DDIDEDP.LIPEAT.G
Retrocopy TGDEASTIAEIIEECGGLEKIEVLQQHENEDIYKLAFGIIDQYFSDDDIDEDPNLIPEAT*G

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_1547 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004850	1 retrocopy	retro_btau_1842,
Rattus norvegicus	ENSRNOG00000014945	1 retrocopy	retro_rnor_987,
Ictidomys tridecemlineatus	ENSSTOG00000003006	1 retrocopy	retro_itri_1777,
Tarsius syrichta	ENSTSYG00000008134	1 retrocopy	retro_tsyr_1547 ,