RetrogeneDB ID: retro_shar_524

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849800.1:197625..197950(-)
• 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_524
TCTGGTCCATTGTGACATACCCTACAATCTGAAACCATATCAACTTTGGTATATGCTGGTAGTAGATTTAGCTTGAAAGA
ACTTCAAGTGTCTGGTATCCATAAAGAAATGGCATGGACCATGGGTATCTTTGTGGATTCCCATCACCAAAATAATTCTA
CAACGTCTCTCCAAATAAATGTGCAGTGGCTGAAAGAATATCATTCCAATCTGATGTTCCTCCCAAGAAACCATCTACAC
TGAAGAAGGGAGATAGTTCTGCTGAAAAACTCAAGTTGGCAATCAGTTTGCACCACTAGTTATGCCCATCAGAAATGTCT
TCAAG

Alignment

ORF - retro_shar_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.41 %
• Parental protein coverage: 52.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
          SGP........T....T.V.AG..FSL.EL.V.GIHK..A.T.GI.VD....N.ST.SLQ.NVQ.LKEY.
Retrocopy SGPL*HTLQSETIS--TLVYAGSRFSLKELQVSGIHKEMAWTMGIFVDSHHQNNSTTSLQINVQWLKEYH

Parental  SKLILFPR-KPSAPKKGDSSAEELKLA-TQLTGPVMPIRNVFK
          S.L...PR.KPS..KKGDSSAE.LKLA..Q....VMPIRNVFK
Retrocopy SNLMFLPR<KPSTLKKGDSSAEKLKLA<NQFAPLVMPIRNVFK

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_524 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 ,