RetrogeneDB ID: retro_shar_256

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL835483.1:10806..11214(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf4
• Ensembl ID: ENSSHAG00000006965
• Aliases: None
• Description: chromosome 12 open reading frame 4 [Source:HGNC Symbol;Acc:1184]

Sequence

>retro_shar_256
GAACATAAACTAGAAGCTTTGGAATCTGGAGATGTTGATGTGTACCAACTGATAAATGTCTGGGCAAAAATTTATACTGA
GAGAACATAAAGACAAGCAAGACTTAAAGAGCCAAGTTGGGAATGAAGATTTTGCAGATGTGTAACAATTCTAAACCATT
CATCTGCCTCTGAAACTCTTAAATTTGGAACACAATTATTTGTTCATTTCTCAGTAGTTATTGGAGAAAGAGATGTGTAA
CTGAAAATGTTAGAAAAAAAGTAACATGTAAAAATGGATAATATAATGCAGGAATTGAGTAACTCACTAACAGATCAGGT
CATAAATTCATTGGCTCCTCAACATTTTGAATCAAAACATATCTTAGAGAATAAATGAACCAGTGAGCTAAAATAGTCAA
TCACCATC

Alignment

ORF - retro_shar_256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.29 %
• Parental protein coverage: 51.89 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EAALEALKSGEVDLHQLTSAWAKTYAETTLEHARPEEPSWD-EDFADV-YHDLIHSPASETLLNLEHNY-
          E..LEAL.SG.VD..QL...WAK.Y.E.T...AR..EPSW..EDFADV.....IH.P....LLNLEHNY.
Retrocopy EHKLEALESGDVDVYQLINVWAKIYTERT*RQARLKEPSWE>EDFADV*QF*TIHLPLK--LLNLEHNY<

Parental  FVSISELIGERDVELKKLRERQGAEMDKVMQELGKSLTDQDVNSLAAQHFESQQVLENKWTSELKQSTAI
          FV..S..IGERDV.LK.L.......MD..MQEL..SLTDQ..NSLA.QHFES...LENK.TSELK.S..I
Retrocopy FVHFSVVIGERDV*LKMLEKK*HVKMDNIMQELSNSLTDQVINSLAPQHFESKHILENK*TSELK*SITI

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_256 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000006965	1 retrocopy	retro_shar_256 ,