RetrogeneDB ID: retro_tsyr_667

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_164358:403..947(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP2K4
• Ensembl ID: ENSTSYG00000011568
• Aliases: None
• Description: mitogen-activated protein kinase kinase 4 [Source:HGNC Symbol;Acc:6844]

Sequence

>retro_tsyr_667
CACTTTTTAAAAACTTTGAAAATTATTCACAAAGATATCAAACCTCCAATATTCTTCTGGACAGAAGTGGAAATATTAAA
CTCTGTGACTTTGGTATCAGTGAACAGCTTGTGGACTTCATTGCCAAGACACGAGATGTCGGTTGTAGGCCATATGTGGC
ACCTGAAAGAATAGACCCAAGTGCATCACAGCAAGGATATGATGTCCGCTGTGATGTCTGGAGTTTGGGGATCACATTGT
ACAAGTTGGTCACAGGCCGATTTCCTTATCCAAAGTGGCATAGTGTATGTGATCAACTAACACAAGTGGTGAAAGGATAT
CCTCCACAGCTGAGTAATTCTGAGGAAAGGGAATTCTCCCCAAGTTTCATAAACTTTGTCAACTTGTACCTTACAAAGGA
TAAATCCAAAAGGCCAAAGTATAAAGAACTTCTGAAAATCCCTTTATTTTGATGTATGAAGAACATATCATTGAGGTCGC
GTGCTATGTTTGTAAAATCCTGGATCAAATGCCAGCTACCCCCAGCTTTCCCATGTATATCGAT

Alignment

ORF - retro_tsyr_667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.87 %
• Parental protein coverage: 50.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HLKENLKIIHRDIKP-SNILLDRSGNIKLCDFGISGQLVDSIAKTRDAGCRPYMAPERIDPSASRQGYDV
          H....LKIIH.DIKP.SNILLDRSGNIKLCDFGIS.QLVD.IAKTRD.GCRPY.APERIDPSAS.QGYDV
Retrocopy HFLKTLKIIHKDIKP<SNILLDRSGNIKLCDFGISEQLVDFIAKTRDVGCRPYVAPERIDPSASQQGYDV

Parental  RSDVWSLGITLYELATGRFPYPKWNSVFDQLTQVVKGDPPQLSNSEEREFSPSFINFVNLCLTKDESKRP
          R.DVWSLGITLY.L.TGRFPYPKW.SV.DQLTQVVKG.PPQLSNSEEREFSPSFINFVNL.LTKD.SKRP
Retrocopy RCDVWSLGITLYKLVTGRFPYPKWHSVCDQLTQVVKGYPPQLSNSEEREFSPSFINFVNLYLTKDKSKRP

Parental  KYKELLK-HPFILMYEERTVEVACYVCKILDQMPATPSSPMYVD
          KYKELLK..PFILMYEE...EVACYVCKILDQMPATPS.PMY.D
Retrocopy KYKELLK<NPFILMYEEHIIEVACYVCKILDQMPATPSFPMYID

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_667 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000065559	1 retrocopy	retro_hsap_4858,
Monodelphis domestica	ENSMODG00000008266	2 retrocopies	retro_mdom_1281, retro_mdom_957,
Mustela putorius furo	ENSMPUG00000003664	1 retrocopy	retro_mputfur_1419,
Pongo abelii	ENSPPYG00000007993	1 retrocopy	retro_pabe_3775,
Tarsius syrichta	ENSTSYG00000011568	1 retrocopy	retro_tsyr_667 ,