RetrogeneDB ID: retro_shar_310

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841297.1:111520..112010(+)
• 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_310
CAAGCAGCTGCGCAAGAATAAAGTTACATTCTCTCTCTCCATGTGTGCGCCAGAATTATACTCAAGAGACTTAAGTACCT
GAGTATTGCTGCAGTTGGTTCCCCCTCTCAGAACTTGACAAGGCATTTTAAAGAGAGTATTAGGTTCATTCATGAATGCC
AACTTAGAGGTGAGGGCTGTCTTACACACTGTCTGGCTGACGTTTCCAGAAGTGTGACCTTCGTGGTTGCTTACATCATG
ATGATTACTGATATCGGCTGGGAAGATGCATGACACATGTTTCGAACTGGAAGGACTTGTGCCAATCCCAACTTGGATTT
CCAGAAGCAGCTCCAGGAGTTTGAAAAAGAATGAAGTTCACCATTTTTGGCAGTAACTAAAAGACGAGTATGGAGAAAAC
CCCTTAAAGGATGCAGAAGAAGCCAAAAACATCCTGGGTAATTACAAAGAGCAAAAACATGCTAAACCACTCCAGCAGAA
TCTTAGTAGG

Alignment

ORF - retro_shar_310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.67 %
• Parental protein coverage: 81.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLSKNKVTHILSIHDSARPMLEGVKYLCIPAADSPSQNLTRHFKESIRFIHECRLRGEGCLVHCLAGVSR
          Q........ILS.H..AR..L...KYL.I.A..SPSQNLTRHFKESIRFIHEC.LRGEGCL.HCLA.VSR
Retrocopy QAAAQE*SYILSLHVCARIILKRLKYLSIAAVGSPSQNLTRHFKESIRFIHECQLRGEGCLTHCLADVSR

Parental  SVTLVVAYIMTITDFGWEDALHMVRAGRSCANPNLGFQKQLQEFE-KNEVHQFRQWLKDEYGEDPLKDAE
          SVT.VVAYIM.ITD.GWEDA.HM.R.GR.CANPNL.FQKQLQEFE.KNEVH.F.Q.LKDEYGE.PLKDAE
Retrocopy SVTFVVAYIMMITDIGWEDA*HMFRTGRTCANPNLDFQKQLQEFE>KNEVHHFWQ*LKDEYGENPLKDAE

Parental  EAKNILARRAPRMKKCSRPLPKKMLR
          EAKNIL........K...PL.....R
Retrocopy EAKNILGNY--KEQKHAKPLQQNLSR

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_310 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,