RetrogeneDB ID: retro_shar_481

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849633.1:1598762..1599002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS3
• Ensembl ID: ENSSHAG00000015012
• Aliases: None
• Description: signal peptidase complex subunit 3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26212]

Sequence

>retro_shar_481
ATAGAAAACGTCATGGGACCTAGAAAATGAAGTGATCTGGGATTCATTACATTTAATGTAACCACTGATCTAGAGAATAT
ATTTGATTGAAATGTAAAGCATTCACTTCTATATCTATCTGCAGAATATCCAATAAAAAATAATTCTCTGAACTAAGTTG
TCCTTTGGGATGAGATTGTTCTGAGAGGTGATAATCCAAAGCTGCTGCTGAATGATGTGAAGTCAAAATATACATATTTT

Alignment

ORF - retro_shar_481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.5 %
• Parental protein coverage: 60.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEDFTGPRERSDLGFITFDVTADLENIFDWNVKQLFLYLSAEYSTKNNALNQVVLWDKIILRGDNPKLLL
          .E...GPR..SDLGFITF.VT.DLENIFD.NVK...LYLSAEY..KNN.LN.VVLWD.I.LRGDNPKLLL
Retrocopy IENVMGPRK*SDLGFITFNVTTDLENIFD*NVKHSLLYLSAEYPIKNNSLN*VVLWDEIVLRGDNPKLLL

Parental  KDMKSKYFFF
          .D.KSKY..F
Retrocopy NDVKSKYTYF

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_481 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000001987	2 retrocopies	retro_mmur_1595, retro_mmur_731,
Oryctolagus cuniculus	ENSOCUG00000029741	1 retrocopy	retro_ocun_119,
Otolemur garnettii	ENSOGAG00000003825	1 retrocopy	retro_ogar_1710,
Pongo abelii	ENSPPYG00000015218	1 retrocopy	retro_pabe_138,
Sarcophilus harrisii	ENSSHAG00000015012	1 retrocopy	retro_shar_481 ,
Ictidomys tridecemlineatus	ENSSTOG00000013678	1 retrocopy	retro_itri_57,