RetrogeneDB ID: retro_shar_831

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867703.1:48442..48893(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000013346
• Aliases: None
• Description: None

Sequence

>retro_shar_831
AGCCCAAGTGGGAAGAAGTTTTGAAGCAAACCTCAGCTTGCCGGTTACCTGGGGAGCTGATGGACCTGAGCACTGTTGAC
TTTCGAACATGGAAAATGATCATGAATAAAATGAACAAGAATCAACAGAGGATGCTCTCTGACTGTTCTAATCAAGCCAA
AGGAAAATCAGATTTAAATACAACACTCCCTTATCGGGCACAGAGCATCTGTCTTCAAAACAGCGTGTTATCAAGATTAC
CAACCATCCCAGTCATAAAGTAAAGAGTGATTCCCAGAAAGCCGTAGACCAGCCTCGACAGCTTTTTGGGGAGAAGAAAC
TAAGTGGACCGAATGTTTTTGACATTGCAGAAGAGCTTGTGAAAACAGTGGACCTACCTAAAGGTTTACAAGGGGTTGGC
TCCGGTTGTACCGATGAAACCCTCCTCTCTGCCATTGCCAGTGCTCTGCAC

Alignment

ORF - retro_shar_831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 58.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SPSGKKFRSKPQLARYLGS-SMDLSTFDFRTGKMLMSKMNKNRQRMRYDCSNQAKGKPDLNTALPVR-QT
          SPSGKKF.SKPQLA.YLGS..MDLST.DFRT.KM.M.KMNKN.QRM..DCSNQAKGK.DLNT.LP.R...
Retrocopy SPSGKKF*SKPQLAGYLGS<LMDLSTVDFRTWKMIMNKMNKNQQRMLSDCSNQAKGKSDLNTTLPYR>HR

Parental  ASIFK-QPVTKITNHPSNKVKSDPQKAVDQPRQLFWEKKLSGLNAFDIAEELVKTMDLPKGLQGVGPGCT
          AS.FK.Q.V.KITNHPS.KVKSD.QKAVDQPRQLF.EKKLSG.N.FDIAEELVKT.DLPKGLQGVG.GCT
Retrocopy ASVFK>QRVIKITNHPSHKVKSDSQKAVDQPRQLFGEKKLSGPNVFDIAEELVKTVDLPKGLQGVGSGCT

Parental  DETLLSAIASALH
          DETLLSAIASALH
Retrocopy DETLLSAIASALH

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_831 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	ENSSHAG00000013346	1 retrocopy	retro_shar_831 ,