RetrogeneDB ID: retro_shar_263

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL835805.1:42198..42780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPG7
• Ensembl ID: ENSSHAG00000015455
• Aliases: None
• Description: spastic paraplegia 7 (pure and complicated autosomal recessive) [Source:HGNC Symbol;Acc:11237]

Sequence

>retro_shar_263
ATGGTACTCAGCTGAAACGGCATGATTCTGAAGCCCCATTTCCACAAAGACTGGCAAAGACAAGGTGCCACATGGTTTAA
CCTGCCAGCCAAGGAGAATAGAATTATAAAAGCCTGTTGAACAAAAGCCCATAAAATTGCTCTTTGCCCAATATCTGGTC
CTATCTGGCCCACTGTCAAGTGCCATACTGTCTGATACCATACTAAAGTACATGTTGGTAGAGGATTCATCTTGGAAGAT
CTTTGGGTGGCTGGTATACATAAAAAGTGGCATGGATCATTGGTATCTCTGTGGATCCTCATTACCAAAATAAGTTTACA
GAGTCTCTCCAGACAAATGTCCAGCAGCTGAAATGATATTATTCCAAACTGATCCTCTTCCCAAGGAAACCATCTGTACT
CAAGAAGAATGATAACTCTGCTGAAGAACTCAAGTTGGCAACCCAGCTCACAGGACTAGTTATGTTCATCAGAAATGTCT
TAAAGAAAGAGAAAGCTTACATCATTAACGAAAAATGAAAAGACTTTCAAGGCATTTGCTAGTTTTTGAATGGCCCAAGC
CAATGCCTGCCTCTGGAATTTG

Alignment

ORF - retro_shar_263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.39 %
• Parental protein coverage: 91.94 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVRCPTVRYHTKV
          M..S.NGMILKPHFHKDWQR..ATWFN.PA...R..KA...KA..IA..P.SGPI.P.V.C.TV.YHTKV
Retrocopy MVLS*NGMILKPHFHKDWQRQGATWFNLPAKENRIIKAC*TKAHKIALCPISGPIWPTVKCHTV*YHTKV

Parental  RAGRGFSLEELRVAGIHKK-VARTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDS
          ..GRGF.LE.L.VAGIHKK.VA..IGISVDP...NK.TESLQ.NVQ.LK.Y.SKLILFPRKPS..KK.D.
Retrocopy HVGRGFILEDLWVAGIHKK<VAWIIGISVDPHYQNKFTESLQTNVQQLK*YYSKLILFPRKPSVLKKNDN

Parental  SAEELKLATQLTGPVMPIRNVFKKEKARVI-TEDEKNFKAFASLRMARANARLFGI
          SAEELKLATQLTG.VM.IRNV.KKEKA..I.T..EK.FKAFAS..MA.ANA.L...
Retrocopy SAEELKLATQLTGLVMFIRNVLKKEKAYII>TKNEKTFKAFASF*MAQANACLWNL

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_263 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000015455	2 retrocopies	retro_shar_263 , retro_shar_524,