RetrogeneDB ID: retro_shar_17

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856797.1:365409..366021(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000007900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017571
• Aliases: None
• Description: None

Sequence

>retro_shar_17
ATGGCGGCCTCATCGGTTCTGGGCGCCGGCCTGGCTCGGATTCTCTTCTATCCGACACTTCTGTACACGCTGGTGCTCGA
TAAGGTGTCAAGAGCCGGGCACCGCGACTGGTACCACCGCATCGACTCTACCGTGCTGCTGGGCGCGCTGCCGCTGCGCA
GTCTCACGCTCCGGCTAGTAGAGAAGGAGAATGTCCGAGCAGTGATCACCATGAATGAAGAATATGAGACGAGGTTCCTG
TGTAACACTTTTGAGGAATGGAAAGCAGTTGGAGTAGAACAACTGCGTCTCAGCACAGTGGATATGACTGGAGTCCCAAC
TTTGGAAAACCTAAAGAAAGGGGTCCAGTTCACACTCAAGTACATGGCCCTGGGGAAATGTGTCTATGTTCACTGCAAGG
CTGGGCGCTCCAGAAGCGCCACCATGGTGGCGGCCTATTTGATACAGGTGTATAACTGGAGTCCCGAGGAGGCCGTGAAA
GCTATTGCTGACATCCGTTCTCACATCCAAATCCGACCTCGGCAGGTAAAAGTTCTCAAGGAATTCCACAGACAGGTCAT
GGCTGAAGCAGAAAAAAACAAGATTTCCCAAAAAGAACTAGCTAACGAATGA

Alignment

ORF - retro_shar_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 96.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLQVTLIEKENVRAVITMNEEYETRFLCNTFEEWKAVGVEQLRLSTVDMTGVPTLENLKKGVQFTLKYMT
          .L...L.EKENVRAVITMNEEYETRFLCNTFEEWKAVGVEQLRLSTVDMTGVPTLENLKKGVQFTLKYM.
Retrocopy SLTLRLVEKENVRAVITMNEEYETRFLCNTFEEWKAVGVEQLRLSTVDMTGVPTLENLKKGVQFTLKYMA

Parental  LGKCVYVHCKAGRSRSATMVAAYLMQVYNWSPEEAVKAIADIRSHIHIRPGQVEVLKEFHKQVIAEAEKT
          LGKCVYVHCKAGRSRSATMVAAYL.QVYNWSPEEAVKAIADIRSHI.IRP.QV.VLKEFH.QV.AEAEK.
Retrocopy LGKCVYVHCKAGRSRSATMVAAYLIQVYNWSPEEAVKAIADIRSHIQIRPRQVKVLKEFHRQVMAEAEKN

Parental  KVSQKEPADE
          K.SQKE.A.E
Retrocopy KISQKELANE

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_17 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000007341	1 retrocopy	retro_pvam_127,
Sarcophilus harrisii	ENSSHAG00000017571	1 retrocopy	retro_shar_17 ,