RetrogeneDB ID: retro_shar_223

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834705.1:41520..41996(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK39
• Ensembl ID: ENSSHAG00000013783
• Aliases: None
• Description: serine threonine kinase 39 [Source:HGNC Symbol;Acc:17717]

Sequence

>retro_shar_223
AAACATGGCAAGTTCCTTAGAAAATTACTTTCATTATGTCTTCAAAAAGATATTTCTAAAAGACCCATAGCAGCAAAACT
TTTAAAATGTAGATTCTTCCAGAAAGCCAAAATAGGGATTAAGTGATTAAAAAACTATTCATGAGGAAACCAAATATAAC
ACAGAGAGCTAAAAAGGTCAGAAAAGTTCCTAGACCCAGAGTCATCTTCACAAGACAGAAGACAAGACTGGGAGTGGATT
GATGACAAAATGGATGAAAAGAATGAAGAAAAAGCAACATTTTCTCAGAAAAAGTCACTAAGAGAAAAAGAAGAAAATCA
AGAGATTATAGTGAATATCAGCAGTATACCTGAATAGATACAGTCACTTTCTATATAGGACTCACAGGTCAGCTTAATAT
TAATAAAGAATTCACAGAAACTTCTTGTGATGTGCTTCTTATTTTAAGATTCAATCAGAACCAGGAGAAAGGAAAT

Alignment

ORF - retro_shar_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.06 %
• Parental protein coverage: 52.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KYGKSFRKLLSLCLQKDPSKRPTAAELLKCKFFQKAK-NREYLIEKLLTRTPDIAQRAKKVRRVPG-SSG
          K.GK..RKLLSLCLQKD.SKRP.AA.LLKC.FFQKAK.NR...I.KL..R.P.I.QRAKKVR.VP.....
Retrocopy KHGKFLRKLLSLCLQKDISKRPIAAKLLKCRFFQKAK<NRD*VIKKLFMRKPNITQRAKKVRKVPR<TQS

Parental  HLHKTED-GDWEWSDDEMDEKSEEGKAAFFQEKSRRVKEENPEITVNASSIPEQIQSLSIKDSK-GQPNI
          HLHKTED..DWEW.DD.MDEK.EE.KA.F.Q.KS.R.KEEN.EI.VN.SSIPE.IQSLSI.DS..GQ.NI
Retrocopy HLHKTED<QDWEWIDDKMDEKNEE-KATFSQKKSLREKEENQEIIVNISSIPE*IQSLSI*DSQ<GQLNI

Parental  HEGFTETSCAVNLVLRLRNSRKELN
          ...FTETSC.V.L.LR........N
Retrocopy NKEFTETSCDVLLILRFNQNQEKGN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_223 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000013783	1 retrocopy	retro_shar_223 ,