RetrogeneDB ID: retro_shar_247

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834847.1:13654..14136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PITPNA
• Ensembl ID: ENSSHAG00000003595
• Aliases: None
• Description: phosphatidylinositol transfer protein, alpha [Source:HGNC Symbol;Acc:9001]

Sequence

>retro_shar_247
AATGGATATATGAAAGATGACTTTTCACAAAGATTGATCAGGCACAAACCAGACTTTGGAACAACAGAAAATGTACTTAA
TTTAGATCCTAACACATGGAAGATGGTTGAAATTGTCCATATGGATATTTCAAACTAATGTCAGATAAAACCTGCAGATT
ACAAATTGAATGAAGACTCAGCACCATACCAATCAGTCAAGACCAAGAAAGGACCCAATTGGAAGAAAGACCTGGTAAAT
AACCAAGACTCTCCTCAAATGTGTGACTATAAGATGGTAACCATCAAATTCAAGTGGTGGGGTCTGCAGAGTAAAGTAGA
AAACTTTATTCAAAAACAAGAAAAAATAATATTAACTTTCACTACCACCTTTTTTGTTGAATTGACAAGTGGATTGCTCT
GACTATTGAAGACATTTGAAAAGCGCAAGTTGAGACCCAGAAAGAGCTAGAAGTTCTATGTAATCAAAATCTAGTGAGGG
GA

Alignment

ORF - retro_shar_247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.5 %
• Parental protein coverage: 84.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEYMKDDFLIKIETWHKPDLGTLENVHKLEPDVWKHVETVFIDIADRSQVLSKDYKQEEDPAKFKSIKTG
          N.YMKDDF.......HKPD.GT.ENV..L.P..WK.VE.V..DI....Q....DYK..ED.A...S.KT.
Retrocopy NGYMKDDFSQRLIR-HKPDFGTTENVLNLDPNTWKMVEIVHMDISN*CQIKPADYKLNEDSAPYQSVKTK

Parental  RGPLGPNWKKELANQKDLPYMCAYKLVTVKFKWWGLQNKVENFIQKQEKRLFTNFHRQLF-CWLDKWVEL
          ....GPNWKK.L.N..D.P.MC.YK.VT.KFKWWGLQ.KVENFIQKQEK...T.F....F.C..DKW..L
Retrocopy K---GPNWKKDLVNNQDSPQMCDYKMVTIKFKWWGLQSKVENFIQKQEKIILT-FTTTFF<C*IDKWIAL

Parental  TMDDIRRMEDETKRQLDEMREKDPVKG
          T..DI.....ET...L........V.G
Retrocopy TIEDI*KAQVETQKELEVLCNQNLVRG

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_247 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000003595	1 retrocopy	retro_shar_247 ,
Ictidomys tridecemlineatus	ENSSTOG00000005039	1 retrocopy	retro_itri_1725,