RetrogeneDB ID: retro_shar_595

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL851186.1:7771..8095(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000003637
• Aliases: None
• Description: None

Sequence

>retro_shar_595
GTGTCACACTTTTCCCGAAAATTGTTGAAAGTCAAACTGGAGGGCGCCAAGCACCTCAAGAAGCTCCAGAACCATCATGG
GGGCCAGATCCTCCTGAAGGCTGTACAAAAACCTGCCCTAGATGAGTGGGACTGCAGTTTTTTCCCCATGGAGGCTGCCC
CAAACCTGGAGAAGGGTCTCAACCAGGCCCTCCTGAAGCTGCAAGCCCTGAACTGAAACCAAAGAGATCCCCAACCTTGC
GATTTTCTGGAAAGCCACTACCTGTGCGAGGAGGTGAAGTTGATGAAGCACCTGACCACCTTGTGCCATGTGCAGGCCAA
CCCT

Alignment

ORF - retro_shar_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.64 %
• Parental protein coverage: 76.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSHFFRELSKDKREGAERLMKLQNQRGGRVLLQAVQKPAQDEWGRSLEAMEAALNLEKGLNQALLKLHAL
          VSHF.R.L.K.K.EGA..L.KLQN..GG..LL.AVQKPA.DEW..S...MEAA.NLEKGLNQALLKL.AL
Retrocopy VSHFSRKLLKVKLEGAKHLKKLQNHHGGQILLKAVQKPALDEWDCSFFPMEAAPNLEKGLNQALLKLQAL

Parental  GSSQGDPQLCDFLESHYLGEEVKLMKRLGNHLTTLRHLQADP
          ...Q.DPQ.CDFLESHYL.EEVKLMK....HLTTL.H.QA.P
Retrocopy N*NQRDPQPCDFLESHYLCEEVKLMK----HLTTLCHVQANP

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_595 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006157	5 retrocopies	retro_meug_1020, retro_meug_1224, retro_meug_1314, retro_meug_1425, retro_meug_349,
Monodelphis domestica	ENSMODG00000013730	3 retrocopies	retro_mdom_1989, retro_mdom_6, retro_mdom_745,
Sarcophilus harrisii	ENSSHAG00000003637	1 retrocopy	retro_shar_595 ,