RetrogeneDB ID: retro_shar_509

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849724.1:120782..121256(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011251
• Aliases: None
• Description: None

Sequence

>retro_shar_509
TGGGAAGTGAAAAGGTTACATAAAATTATTCAGGAAAAGAAGCAAAAGAAGGAACAGTAAGAGAAGGGAGAGTAAAACAC
ATTACAAATTCTGATGATCAGGATTCCAGTTGAAATGTCCTTAAAGAGGAGAACTAAGAGATCACAACATGGACATAACA
ATCAGAAAGTTCACTTTATAAAATGGAAGATTCTGTTGAAGATTGAAATGAAGAAGATGACTTCTTGTAATCAAACCAAC
TGAGCAATTGTCACATAAGGAAAAAAAAAGTTTGTCAAGGAAAGATGAGAAAAGAAAAGGAAAACACCAGCATCACAGTT
GCTAAGGTGATAGCAAGAAGCATGTCAGGATGAAGAACAGAAGAAGGAACAAAAGCATGAGAAAAGTTATTGAGAGTGGC
AGGCTAAAACTCAGAAGGAATGGGAAAGGCAGAAATTAAGGGAAATGGCTTCAGAAGTGTCCAGTTGGGAGAGA

Alignment

ORF - retro_shar_509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.33 %
• Parental protein coverage: 95.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  WKVKTLDEILQEKKRRKEQEEKAE-IKRIKNSDDRDSKRDSLEE-GELRDHRMEITIR-NSPYRREDSME
          W.VK.L..I.QEKK..KEQ.EK.E..K.I.NSDD.DS....L.E.GELRDH.M.ITIR..S.Y..EDS.E
Retrocopy WEVKRLHKIIQEKKQKKEQ*EKGE<VKHITNSDDQDSS*NVLKE<GELRDHNMDITIR>SSLYKMEDSVE

Parental  DRGEEDDSL-AIKPPQQMSRKEKAH-HRKDEKRKEKRRHRSHSAEGVGKHARVK-EKEREHERRKRHREE
          D..EEDD.L..IKP..Q.S.K......RKDEKRK.K..H.S.......KH.R.K.E...E....K...E.
Retrocopy D*NEEDDFL<VIKPTEQLSHKXXXXLSRKDEKRKGKHQHHSC*GDSK-KHVRMK<EQKKEQKHEKSY*EW

Parental  QDKARREWERQKRREMAREHSRRER
          Q.K...EWERQK.REMA.E.S..ER
Retrocopy QAKTQKEWERQKLREMASEVSSWER

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_509 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000046253	1 retrocopy	retro_rnor_2850,
Sarcophilus harrisii	ENSSHAG00000011251	3 retrocopies	retro_shar_219, retro_shar_371, retro_shar_509 ,