RetrogeneDB ID: retro_tsyr_1622

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_514402:4..1006(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLS3
• Ensembl ID: ENSTSYG00000006670
• Aliases: None
• Description: plastin 3 [Source:HGNC Symbol;Acc:9091]

Sequence

>retro_tsyr_1622
GTGGTTACTACTCAGATCTCCAAGATGAGCTTGATGGACTCAAAGAGGCCCTTTGCAAAAGTTGATCTCAACAGCAACGA
ATTCATTCGTGACTATGAACTTCATGAGCTTTTCAAGGAAGAGAATATGTCATTTCTGGGACATAAAGTGAGAGGAATTA
CTCAGAAGCTCATGCTGGATGGTGACAGGAATAAAGATGGGAAGATAAGTTTTGATGAATTTGTTTATATTTTTTAAGAG
GTCAGAAGCAGTGATATTGCCAATCCCTTCCACAAAGCAATCAACAGGAAATAAGGTATTTGTGCTCTGGGAGGAACTTC
GGTGTTGTCCAGTGAAGGAACACAGCATTCTTACTCAGAGGAAGAAAAATATGCTTTTGTTAACTGGATAAACAAAGATT
TGGAAAATGATCCTGATTGCAGACATGTTATACCAATGAACCCAAACATCGATGACCTGTTCAAAGCTGTTAGTGATGGA
ATTGTGCTTTGTAAAATGATAGACCTTTCAGTCCCTGATACAATTGATGAAAGAGCAATCAACAAGAAGAAACTTACACC
ATTCCTCATTCAAGAAAACTTGAACTTAGCACTGAACTCTGCTTCTGCTATTGGATGTCACGTTGTGAACACTGGTGCAG
AGGATTTGCAGGCAGAGAAACCTCATCTTGTGTTGGGACTGCTTTGGCAAATCATGAAGATCAGTTTGTTTGCTGGGATA
AAATTAAGCAGGAATGAAGCCTTGGCTTCATTGCTCTGAGATGGTGAGAATTTGGAGGAACTTATGAAATTGTCTCCAGA
AGAGCTTCTGCTTAGACGGGCAAACTTTCATTTGGAAAACTCAGGCTGACATAAAATCAACAACTTTAGTGCTGACATCA
AGGATTTCAAAACCTATTTCCATCTTCTCAATCAAATTGCACCAAAAAGGACAAATGGAAAGGTGAACCACGGATAGATA
TTTAACATGTCAGGTTTCAATGATACAGATGATTTCTAGAGA

Alignment

ORF - retro_tsyr_1622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.07 %
• Parental protein coverage: 52.63 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MATTQISK-DELDELKEA-FAKVDLNSNGFICDYELHELFKEANMPLPGYKVREIIQKLMLDGDRNKDGK
          ..TTQISK.DELD.LKEA.FAKVDLNSN.FI.DYELHELFKE.NM...G.KVR.I.QKLMLDGDRNKDGK
Retrocopy VVTTQISK<DELDGLKEA>FAKVDLNSNEFIRDYELHELFKEENMSFLGHKVRGITQKLMLDGDRNKDGK

Parental  ISFDEFVYIFQEVKSSDIAKTFRKAINRKEGICALGGTSELSSEGTQHSYSEEEKYAFVNWINKALENDP
          ISFDEFVYIF.EV.SSDIA..F.KAINRK.GICALGGTS.LSSEGTQHSYSEEEKYAFVNWINK.LENDP
Retrocopy ISFDEFVYIF*EVRSSDIANPFHKAINRK*GICALGGTSVLSSEGTQHSYSEEEKYAFVNWINKDLENDP

Parental  DCRHVIPMNPNTDDLFKAVGDGIVLCKMINLSVPDTIDERAINKKKLTPFIIQENLNLALNSASAIGCHV
          DCRHVIPMNPN.DDLFKAV.DGIVLCKMI.LSVPDTIDERAINKKKLTPF.IQENLNLALNSASAIGCHV
Retrocopy DCRHVIPMNPNIDDLFKAVSDGIVLCKMIDLSVPDTIDERAINKKKLTPFLIQENLNLALNSASAIGCHV

Parental  VNIGAEDLRAGKPHLVLGLLWQIIKIGLFADIELSRNEXXXXXXXXXXXXEELMK-SPER-ALRWANCHV
          VN.GAEDL.A.KPHLVLGLLWQI.KI.LFA.I.LSRNE............EELMK.SPE...LR.AN.H.
Retrocopy VNTGAEDLQAEKPHLVLGLLWQIMKISLFAGIKLSRNEALASLL*DGENLEELMKLSPEELLLRRANFHL

Parental  ENSGWQKINN-SADIKDSKAYFHLLNQIAP-KGQKE-GEPRIDI-NMSGFNETDDLKR
          ENSG..KINN.SADIKD.K.YFHLLNQIAP.KGQ.E.GEPRIDI.NMSGFN.TDD..R
Retrocopy ENSG*HKINNFSADIKDFKTYFHLLNQIAP>KGQME>GEPRIDI>NMSGFNDTDDF*R

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_1622 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000015252	1 retrocopy	retro_ogar_1707,
Tarsius syrichta	ENSTSYG00000006670	1 retrocopy	retro_tsyr_1622 ,