RetrogeneDB ID: retro_tsyr_1987

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_75077:9872..10870(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NLK
• Ensembl ID: ENSTSYG00000008815
• Aliases: None
• Description: nemo-like kinase [Source:HGNC Symbol;Acc:29858]

Sequence

>retro_tsyr_1987
AAACATGATAATGTACTCTCTGCCCTTGACATACTCCAACCTCCACACATTGACTATTTTGAGGAAATATATGTTGTCAC
AGAATTGATGCAAAATGACCTACATAAAATTATCATTTCTCCTCAACCACTCAGCTTAAATCATGTCCAAGTTTTTCTTT
ATCAGATTTTGCGAGGTTTGAGCTATCTCCATTCAGCTGTCATTTTACATCAAGACATTAATCCAGGGAATCTCCTTATG
AACAGCAACTGTATTCTAAAGATTTGTGATTTTGGATTGGCCAGAGTGGAAGAATTAGATAAATCCCGTCATATGACTCA
GCAAGTTGTCACTCTGTATTATAGGGCTCCGGAAATCCTGATGGGTAACCATCATCACAGCAATGCTATTGACATCTGGT
CTGTCAGATGTATCTTTGCAGAACTATTAGGATGAAGAATATTGTTTCAGGCACAGAGTCCCATTCAGCAGTTGGATTTG
ATCACGGATCTGTTGGGCACACCATCACTGGAAGCAATGAGGACGGCTTGTGAAGGTGCTGAGGCACATATACTCAGGGG
TCCTCATAAACAGCCATCTCTTTCTGTACCCTATACCCTGTCTAGCCAGGCTACTCACGAAGCTGTTCGCAAGATGTTGG
TCTTTGATCCATCCAAAAGAATATCCACTAAGAATATGCCTTAGCCCACCCCTACCTAGATGAAGGGTGACTACCCTATC
ACACATGTATGAATAAATGTTGCTTTTCCACCTCTACTGGAAGAGTTTATACCAGTGACTTTGAGCCCATCACAAATCCC
AAATATGATGACACTTTTGAGAAGAACCTCGGTTCTGTCCGACAGGTTAAAGAAATTATTCACCAGTTCATTTTGGAACA
GCAGGAAGGAAACAGAGTACCTTTCTGCATCAACCCTCAGTCTGCTGCTTTTAAGAGCTTTATTAGTTCCACTGTTGCTC
AACTCCCTGAGATACCCCCATCTCCTCTGGTGTGGGAG

Alignment

ORF - retro_tsyr_1987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.94 %
• Parental protein coverage: 63.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KHDNVLSALDILQPPHIDYFEEIYVVTELMQSDLHKIIVSPQPLSSDHVKVFLYQILRGLKYLHSAGILH
          KHDNVLSALDILQPPHIDYFEEIYVVTELMQ.DLHKII.SPQPLS..HV.VFLYQILRGL.YLHSA.ILH
Retrocopy KHDNVLSALDILQPPHIDYFEEIYVVTELMQNDLHKIIISPQPLSLNHVQVFLYQILRGLSYLHSAVILH

Parental  RDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIFA
          .DI.PGNLL.NSNC.LKICDFGLARVEELD.SRHMTQ.VVT.YYRAPEILMG..H.SNAIDIWSV.CIFA
Retrocopy QDINPGNLLMNSNCILKICDFGLARVEELDKSRHMTQQVVTLYYRAPEILMGNHHHSNAIDIWSVRCIFA

Parental  ELLGRRILFQAQSPIQQLDLITDLLGTPSLEAMRTACEGAKAHILRGPHKQPSLPVLYTLSSQATHEAVH
          ELLG.RILFQAQSPIQQLDLITDLLGTPSLEAMRTACEGA.AHILRGPHKQPSL.V.YTLSSQATHEAV.
Retrocopy ELLG*RILFQAQSPIQQLDLITDLLGTPSLEAMRTACEGAEAHILRGPHKQPSLSVPYTLSSQATHEAVR

Parental  LLCRMLVFDPSKRISAKD-ALAHP-YLDEGRLRYHTCMCKCCFSTSTGRVYTSDFEPITNPKFDDTFEKN
          ....MLVFDPSKRIS.K...L..P.YLDEG.L.YHTCM.KCCFSTSTGRVYTSDFEPITNPK.DDTFEKN
Retrocopy ---KMLVFDPSKRISTKN>CLSPP>YLDEG*LPYHTCMNKCCFSTSTGRVYTSDFEPITNPKYDDTFEKN

Parental  LSSVRQVKEIIHQFILEQQKGNRVPLCINPQSAAFKSFISSTVAQPSEMPPSPLVWE
          L.SVRQVKEIIHQFILEQQ.GNRVP.CINPQSAAFKSFISSTVAQ..E.PPSPLVWE
Retrocopy LGSVRQVKEIIHQFILEQQEGNRVPFCINPQSAAFKSFISSTVAQLPEIPPSPLVWE

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_1987 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000008904	1 retrocopy	retro_ptro_2845,
Rattus norvegicus	ENSRNOG00000008704	1 retrocopy	retro_rnor_952,
Tarsius syrichta	ENSTSYG00000008815	1 retrocopy	retro_tsyr_1987 ,