RetrogeneDB ID: retro_shar_283

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841201.1:1098027..1098549(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM150A
• Ensembl ID: ENSSHAG00000016184
• Aliases: None
• Description: transmembrane protein 150A [Source:HGNC Symbol;Acc:24677]

Sequence

>retro_shar_283
GTGGCCTTAGTCTTCTTTCTCCACCATGGCCAGAGTCACTGGTCCTGGGCTTAGCACCACTGCTCCCATCCCAGGCTGCT
TTGATGCTGGTTGCCTGGTAGTTGTTGGCAACTTCTAAGTGGAGTCTTTACACTATATCAGGGCAGGAGTCACCATCCCA
GTGGACCTCCTCTTTGTCCCCACTATGTTTTCTGCTACCGTGGTGCTGCTGTTCCCCGTAACTTTGCCATGGCTCACTTC
CGTGCTGTACTCATTGTTATTGCCTTTGTGGCCATGTTTCTCTGTGGTATCTTCTTCATCCAGGAACACTAGCAGCTCCA
TCACACGGCTGCCCTGTCCAAGGGGGTTTTCATCATTGACATCTTCATTTTCCATGGCACCTTCGCCTATGAGTTTGGGT
TGGTGTCCACAGACACATTGGGAGCTGCCTTCCAGCCATCCCCCAGCCAAACCTGCAAGTCTCCAGGGAGCAGTAGCCCT
CCACTTAACCTGAACTGCATACCTGAAAGTATTGCCATGATA

Alignment

ORF - retro_shar_283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.04 %
• Parental protein coverage: 67.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VALVCLLRYGQLLEQSHRSW-VNTMALITGCFNAAGLVVVGNFQVDHAKSLHYIGAGVAF-PAGLLFVCL
          VALV..L..G....QSH.SW...T.A.I.GCF.A..LVVVGNF.V....SLHYI.AGV...P.G....C.
Retrocopy VALVFFLHHG----QSHWSW>LSTTAPIPGCFDAGCLVVVGNF*VE---SLHYIRAGVTI<PSGPP-LCP

Parental  HCALSYHGAAAPLDFAMAHFRAVLAVIAFVALVLSGIFFIHESSQLQHVAALSEWVFVIDILVFYGTFSY
          H....Y.GAA.P..FAMAHFRAVL.VIAFVA..L.GIFFI.E..QL.H.AALS..VF.IDI..F.GTF.Y
Retrocopy HYVFCYRGAAVPRNFAMAHFRAVLIVIAFVAMFLCGIFFIQEH*QLHHTAALSKGVFIIDIFIFHGTFAY

Parental  EFGAVSTETLVAAFQPAPSRACKSPGSSSTSTHLNCTPESIAMI
          EFG.VST.TL.AAFQP.PS..CKSPGSSS....LNC.PESIAMI
Retrocopy EFGLVSTDTLGAAFQPSPSQTCKSPGSSSPPLNLNCIPESIAMI

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_283 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000016184	1 retrocopy	retro_shar_283 ,