RetrogeneDB ID: retro_shar_270

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841145.1:114446..114715(+)
• Located in intron of: ENSSHAG00000002254

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM1
• Ensembl ID: ENSSHAG00000006127
• Aliases: None
• Description: LYR motif containing 1 [Source:HGNC Symbol;Acc:25074]

Sequence

>retro_shar_270
CTCAGAGAAAAGCAGTATGTGATAAATAAAGCAAGAATGTAGCTCCAGAAAAACAAAGATCTTAATATAATCATAACTAC
TAAAATAATATATAGATGAATGCACATCAAGAATTGAAATAGAAATGCTTTTTCAGATCTTATATCTAAGCCCAATTCAC
CTTCCTCTAATGGCTCTGACTCCCCTACAAATTAGTGGACTTCAAAGCTAGGAGAAGCTTAGAAAACTTTCCAGATCATT
ATTATCTCAACTCTCACAATGAAGATTCT

Alignment

ORF - retro_shar_270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.93 %
• Parental protein coverage: 72.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IREKQYIINEARTLFQKNKNLTD-SELIKQCIDECTARIEIGLHYQIPYPRPIHLPPMALTPLQSRGLQS
          .REKQY.IN.AR...QKNK.L...S.L.K..IDECT.RIEI....QI.Y..PIHLP.MALTPLQ..GLQS
Retrocopy LREKQYVINKARM*LQKNKDLNI>S*LLK*YIDECTSRIEIEMLFQILYLSPIHLPLMALTPLQISGLQS

Parental  QEKLRKLSKPL-YLKSHNEVS
          .EKLRKLS..L.YL.SHNE.S
Retrocopy *EKLRKLSRSL>YLNSHNEDS

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_270 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 3 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008951	1 retrocopy	retro_cpor_873,
Monodelphis domestica	ENSMODG00000007076	3 retrocopies	retro_mdom_1844, retro_mdom_721, retro_mdom_807,
Sarcophilus harrisii	ENSSHAG00000006127	6 retrocopies	retro_shar_156, retro_shar_270 , retro_shar_709, retro_shar_795, retro_shar_798, retro_shar_801,