RetrogeneDB ID: retro_shar_117

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842519.1:12484..13234(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000001525
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000004172
• Aliases: None
• Description: None

Sequence

>retro_shar_117
GAGATGGTGGCGCTGGCCAGCAGTCTGATCCGGCAGAAAAGAGAGGTACCAGACCCTGGGACAAGCAGACAGGTGTCAGC
CCAATGGCGAGTGTGTCCGAGGGGTACTAAGTCCTTGTGTCAGAAACAGATATTGATTCTGCTCTCCAAAGTCCGTCTGT
GTGTGGGGCGACGGGCACGGCTGGACAGGGCACCGGAACCTCAACTCAAAGGCATCATCACAAAGCTTTTCTGCCGTCAA
GGTTTCTATCTCTGGGCTAATCCAGATGGGAGCATCAATGGGACACAAGAGGATACCAGCTCTTTCACTCAGTTTAAACT
GATCGCTGTGGGTCTCCGAGTCGTCACTATCCAGAGCACCAAGCTGGGGCCCTATGTAGCCATGAAAGCTGAGGGGCTAC
TCTACAGTTCGCCACACTTTACAGCAGAGTGTCGCTTTAAGGAGTGTGTCTTTGAGAACTATTATGTCCTCTATGCCTCT
GCCCTCTACCGCCAGCGTCGTTCAGGCCGAGCCTGGTATTTAAGTTTGCACAAGGAAGGCCATGTCATGAAAGGAAATAG
AGTCAAGAAGATCAAAGCGACTGCCCATTTTGTGCCTAATCTCCTCGAAGTGGCCATGTACCCGGAGCCTTCCCTGCACA
ATGTACCTGAGATGTCTCCTGCAAATGGCAAGCCTCCTCCAGCCTCTTTGCCTCCTGAAACAACGCTGATGTCTGGGACC
ACCCTTCAAGTCTTCCATCAAGACAGCCAT

Alignment

ORF - retro_shar_117 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALASSLIRQKREVRDPGTSRPVSAQRRVCPRGTKSLCQKQILILLSKVRLCGGRRARPDRAPEPQLKG
          M.ALASSLIRQKREV.DPGTSR.VSAQ.RVCPRGTKSLCQKQILILLSKVRLC.GRRAR.DRAPEPQLKG
Retrocopy MVALASSLIRQKREVPDPGTSRQVSAQWRVCPRGTKSLCQKQILILLSKVRLCVGRRARLDRAPEPQLKG

Parental  IITKLFCRQGFYLQANPDGSINGTQEDTSSFTQFNLIPVGLRVVTIQSTKLGHYVAMNAEGLLYSSPHFT
          IITKLFCRQGFYL.ANPDGSINGTQEDTSSFTQF.LI.VGLRVVTIQSTKLG.YVAM.AEGLLYSSPHFT
Retrocopy IITKLFCRQGFYLWANPDGSINGTQEDTSSFTQFKLIAVGLRVVTIQSTKLGPYVAMKAEGLLYSSPHFT

Parental  AECRFKECVFENYYVLYASALYRQSRSGRAWYLGLDKEGHVMKGNRVKKTKAAAHFVPKLLEVAMYREPS
          AECRFKECVFENYYVLYASALYRQ.RSGRAWYL.L.KEGHVMKGNRVKK.KA.AHFVP.LLEVAMY.EPS
Retrocopy AECRFKECVFENYYVLYASALYRQRRSGRAWYLSLHKEGHVMKGNRVKKIKATAHFVPNLLEVAMYPEPS

Parental  LHNVPETSPANDKPPPAS
          LHNVPE.SPAN.KPPPAS
Retrocopy LHNVPEMSPANGKPPPAS

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_117 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
Oryctolagus cuniculus	ENSOCUG00000004215	1 retrocopy	retro_ocun_736,
Sarcophilus harrisii	ENSSHAG00000004172	1 retrocopy	retro_shar_117 ,