RetrogeneDB ID: retro_shar_532

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849842.1:3560206..3560534(+)
• Located in intron of: ENSSHAG00000018311

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM1
• Ensembl ID: ENSSHAG00000017260
• Aliases: None
• Description: LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:20472]

Sequence

>retro_shar_532
ATTGATAAGAAATATCTGTGACTCCTTTGAGGTGGTAGAATCCTTATAGGCTATTTGCAAAGCATGAATCAATTTGCTAA
TTATTATTACACCAAAATGTGGAACACATTCTTGTGTGCCAAAAGTATGGCAATATATCTCAAGAGATTTTTGTTGTCCT
AGGAGAAAATGTGGTCCCTTCTAATAGAAATAGGCCTGGAGAAGCAAAGTAACACTCCTCTCAAGCAAGTTATCTATTGA
GGAAATCCTGGGAGAAGAAAGAAGAAAGAAGAAAGAAGAAAAAAAGCAGACTAAGCAGGAAGCAGAGAAGCTAAAAGTCC
AAGCTCTC

Alignment

ORF - retro_shar_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.25 %
• Parental protein coverage: 81.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IDKKHLVLLRDGRTLIGYLRSIDQFAN-LVLHQTVERIHVGKKYGDIPRGIFVVRGENVV-LLGEIDLEK
          IDKK.L.LL..GR.LIGYL.S..QFAN.L.LHQ.VE.I.V..KYG.I...IFVV.GENVV.LL.EI.LEK
Retrocopy IDKKYL*LL*GGRILIGYLQSMNQFAN<LLLHQNVEHILVCQKYGNISQEIFVVLGENVV>LLIEIGLEK

Parental  ESDTPLQQV-SIEEILEEQRVEQQTKQEAEKLKVQALKERGL
          .S.TPL.QV.SIEEIL..............K.....LK...L
Retrocopy QSNTPLKQV>SIEEILXXXXXXXXXXXXQTKQEAEKLKVQAL

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_532 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011141	1 retrocopy	retro_amel_263,
Myotis lucifugus	ENSMLUG00000003734	1 retrocopy	retro_mluc_723,
Mustela putorius furo	ENSMPUG00000009883	1 retrocopy	retro_mputfur_490,
Mus musculus	ENSMUSG00000037296	1 retrocopy	retro_mmus_3725,
Oryctolagus cuniculus	ENSOCUG00000015399	1 retrocopy	retro_ocun_1276,
Sarcophilus harrisii	ENSSHAG00000017260	1 retrocopy	retro_shar_532 ,