RetrogeneDB ID: retro_shar_818

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867574.1:2245626..2245955(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX4
• Ensembl ID: ENSSHAG00000000917
• Aliases: None
• Description: sorting nexin 4 [Source:HGNC Symbol;Acc:11175]

Sequence

>retro_shar_818
GAACAGTGTGAAGAACTCGCCACAGGAACTGCGAGAACACTCTCCCTATAAGGAATGACTACTGAACCGTCTGGTCAAGA
AAGCACAGAGCAAAGAGAAGCCAGAATAAAGGTACTAGAAGAACAAATAAATGAAGGAGAACAGCAGAAGTTACAAATCT
GGAAGGCGGAGAATTTGTGAAAGCTGCTCGGGCAGATGTCCAATGTTTCAAAGAGCAAAAGCACCACGATTTAAAGAAGG
CTCTCATAAGCTACGTCCCTATGCTTCCCAGTATGTGCAAAAAGGGAATTCAAGGGTGGACCAATGTTAAAGAATACTTC
GGCAATATG

Alignment

ORF - retro_shar_818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.32 %
• Parental protein coverage: 62.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QQCEELATGTVRTFSLKGMTSKLFGQETPEQREARIKVLEEQINEGEEQLKSK-NLEGREFVKAAWADIE
          .QCEELATGT.RT.SL.GMT....GQE..EQREARIKVLEEQINEG.EQ.K...NLEG.EFVKAA.AD..
Retrocopy EQCEELATGTARTLSL*GMTTEPSGQESTEQREARIKVLEEQINEG-EQQKLQ<NLEGGEFVKAARADVQ

Parental  RFKEQKNHDLKEALISYAVMQISMCKKGIQVWTNAKECFSKM
          .FKEQK.HDLK.ALISY..M..SMCKKGIQ.WTN.KE.F..M
Retrocopy CFKEQKHHDLKKALISYVPMLPSMCKKGIQGWTNVKEYFGNM

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_818 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022808	1 retrocopy	retro_mmus_1627,
Sarcophilus harrisii	ENSSHAG00000000917	1 retrocopy	retro_shar_818 ,
Sarcophilus harrisii	ENSSHAG00000002487	1 retrocopy	retro_shar_420,
Tursiops truncatus	ENSTTRG00000014983	1 retrocopy	retro_ttru_398,