RetrogeneDB ID: retro_shar_372

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841531.1:25966..26432(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORMDL3
• Ensembl ID: ENSSHAG00000014339
• Aliases: None
• Description: ORM1-like 3 (S. cerevisiae) [Source:HGNC Symbol;Acc:16038]

Sequence

>retro_shar_372
AAAATGAATGTTGAAGTTGCTCACACTGAGGTAAATATAAATACCAGGTAATAAGCAGTTGTGACATATGGCTGATATGC
TTCTTTGGGAATTGGTTTGCTTCATATTGTCTTCAGCATATTGTCTCAACATTTCCTTCTTCAGTGTCTCTGTTGTTTGG
ATATTAATGGATATTATACGTACTCTGAGAATGTATTTTTATATTCAGTAAGAGGAATACCTTTTCAAACTCTTGACAAG
GTGAAACCAGGCTGCTAATTCACTAAGGACAACTGAACTATGGAATAGAGTTTACTTCTTGAGAAAATTTGTCACAATTT
TTCCAATAATTCTACATTTTCTGGCAAGTTTCTACACCAAGGATGATCCTACACAATTCTTCTTAAACACAGTTTCTCTC
CTAAGTGTACTAATTCCTCCAAAACCACAACTGCATAATGTTCAGATCTTTGGTATTAATAAGTAC

Alignment

ORF - retro_shar_372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.38 %
• Parental protein coverage: 95.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KMNVGTAHSEVNPNTR-VMNSRGIWLSYV-LAIGLLHVV--LLSIPFVSVPVVWTLTNLIHNMGMYIFLH
          KMNV..AH.EVN.NTR.V..S..IWL....L.IGLLH.V...LS..F..........N.........FL.
Retrocopy KMNVEVAHTEVNINTR<VISSCDIWLICF>LGIGLLHIVFSILSQHFLLQCLCCLDINGYYTYSENVFLY

Parental  TVKGTPFETPD-QGKARLLTHWEQMDYGVQFTA-SRKFLTITPIVLYFLTSFYTKYDQLHFILNTVSLMS
          .V.G.PF.T.D.QG..RLL.H..Q..YG..FT...RKF.TI.PI.L.FL.SFYTK.D...F.LNTVSL.S
Retrocopy SVRGIPFQTLD<QGETRLLIH*GQLNYGIEFTS<LRKFVTIFPIILHFLASFYTKDDPTQFFLNTVSLLS

Parental  VLIPKLPQLHGVRIFGINKY
          VLIP..PQLH.V.IFGINKY
Retrocopy VLIPPKPQLHNVQIFGINKY

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_372 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000031660	1 retrocopy	retro_fcat_730,
Macropus eugenii	ENSMEUG00000000957	3 retrocopies	retro_meug_1234, retro_meug_130, retro_meug_2052,
Mus musculus	ENSMUSG00000038150	1 retrocopy	retro_mmus_2464,
Sarcophilus harrisii	ENSSHAG00000014339	1 retrocopy	retro_shar_372 ,