RetrogeneDB ID: retro_shar_241

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834751.1:1208220..1208723(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP22
• Ensembl ID: ENSSHAG00000015165
• Aliases: None
• Description: dual specificity phosphatase 22 [Source:HGNC Symbol;Acc:16077]

Sequence

>retro_shar_241
ATTGGGAATGTAGTGAACAATATTCTCCCTGGCATCTACATTGACAACTTTGAAGATATAAAAGTTGCAGAGTACCTGAG
CAAGGATAAAGTTATACCCATTTTCTCTATCCATAATGGCACTAGACCTATGCTTAAAGGAATTAAATACCTATGTATTC
CTGCTGCTGATTCACTGCCCCAGAACTTAAGAAGATATTTTAAAGAAAGTATTGGGTTCATTCATGAGAGCCAGCTTAGA
GGTTAAGATTCTCCTGTACACTGCCTGGATAGTGTTTCCAGAAATAAGATCTTAGAGGTTGCTTATATTATGACGATTAC
AAACTTGGGAAGATGCACAACAAACACATAGTTAAAGCAGGAGGGTCTTGTGCTGACCTCAACTTGGGCTTCCAAGAGCA
GTTCCATGAGTTTGAAAAGAATCAACTTCACCTATTTTGGCTATGACTAAAAGGTAAATATGAAGAAAACCATTCAAAGG
ATGAAGAAACCAAAAATATTTTG

Alignment

ORF - retro_shar_241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.59 %
• Parental protein coverage: 83.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGNGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSIHDSARPMLEGVKYLCIPAADSPSQNLTRHFKES
          .GN..N.ILPG.YI.NF.D...AE.LSK.KV..I.SIH...RPML.G.KYLCIPAADS..QNL.R.FKES
Retrocopy IGNVVNNILPGIYIDNFEDIKVAEYLSKDKVIPIFSIHNGTRPMLKGIKYLCIPAADSLPQNLRRYFKES

Parental  IRFIHECRLRGEGCLVHCLAGVSRSVTLVVAYIMTITDF-GWEDALHMVRAGRSCANPNLGFQKQLQEFE
          I.FIHE..LRG....VHCL..VSR...L.VAYIMTIT...G.....H.V.AG.SCA..NLGFQ.Q..EFE
Retrocopy IGFIHESQLRG*DSPVHCLDSVSRNKILEVAYIMTITNL<GKMHNKHIVKAGGSCADLNLGFQEQFHEFE

Parental  KNEVHQFRQWLKDEYGEDPLKDAEEAKNIL
          KN..H.F...LK..Y.E...KD.EE.KNIL
Retrocopy KNQLHLFWL*LKGKYEENHSKD-EETKNIL

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_241 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011289	1 retrocopy	retro_etel_1581,
Rattus norvegicus	ENSRNOG00000018218	2 retrocopies	retro_rnor_858, retro_rnor_887,
Sarcophilus harrisii	ENSSHAG00000015165	2 retrocopies	retro_shar_241 , retro_shar_310,
Tursiops truncatus	ENSTTRG00000001848	1 retrocopy	retro_ttru_668,