RetrogeneDB ID: retro_shar_175

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834538.1:943792..944215(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLA2G10
• Ensembl ID: ENSSHAG00000009421
• Aliases: None
• Description: phospholipase A2, group X [Source:HGNC Symbol;Acc:9029]

Sequence

>retro_shar_175
TTGCTACTACTGCTCTTCACAACTGTTTCAGGGAAATCGCATGTGCATCAGAGGGAACTCTTGGAGCTGGCAGAAGCTCT
CAATTGTGTTACAAGCTACTCAGCATTTGTTTATGTGAGCTATGGCTGCTACTGTAGCATTGGAGGAACTGGTTGGCCAC
AAGACCAAATTGACTGACGTTGCCAAAAACATGACTGCTGTTATAGCAAGGTTGAGAAAGCTGGTTGTGGCCCCAAAACA
GAACTTTATAACCAGAAATGCACAGACCAGAGGATATAATGTGATGCCAACCTGAACAAATGCCAAGAAATGATGTGCAA
ATGTGACAAGGAAATTGCTCACAGTTTGGTCACAGCAAAATATAATACAAAGTAAATTTTCTTTCTCCATTTCCTTTGTG
GAGATAGGAAGCCTAAGTGTGAC

Alignment

ORF - retro_shar_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.05 %
• Parental protein coverage: 87.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLSLPLPLVSGKSHVHRRGLLELAGALSCATSRSALAYVSYGCYCGLGGTGWPKDQTDWCCQKHDCCYSK
          LL.L....VSGKSHVH.R.LLELA.AL.C.TS.SA..YVSYGCYC..GGTGWP.DQ.D..CQKHDCCYSK
Retrocopy LLLLLFTTVSGKSHVHQRELLELAEALNCVTSYSAFVYVSYGCYCSIGGTGWPQDQID*RCQKHDCCYSK

Parental  VEEAGCGPKTERYDWKCTDQKVECNADLNTCQEMMCKCDMEIAHCLATAKYNQKLIFFPHFLCGNKTPKC
          VE.AGCGPKTE.Y..KCTDQ...C.A.LN.CQEMMCKCD.EIAH.L.TAKYN.K.IFF.HFLCG...PKC
Retrocopy VEKAGCGPKTELYNQKCTDQRI*CDANLNKCQEMMCKCDKEIAHSLVTAKYNTK*IFFLHFLCGDRKPKC

Parental  D
          D
Retrocopy D

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_175 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000009421	1 retrocopy	retro_shar_175 ,