RetrogeneDB ID: retro_shar_277

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841186.1:425638..426083(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLSCR5
• Ensembl ID: ENSSHAG00000017048
• Aliases: None
• Description: phospholipid scramblase family, member 5 [Source:HGNC Symbol;Acc:19952]

Sequence

>retro_shar_277
ACTAATAACACTGGTCAATAGATGTTTACAGTTCACAGATGATTGAGTTGTACCAGCTGCTGGTGCCTTTGCCACCTGAA
AGAGTTAGAAATTCAAGCCCCTCCTGGCACAATATTAGATTATGTTGTATAGAAATAGGAACCTTCCCTGACAGAATTCA
CAATTTAAAATAAAGCAAAGAAAATATGTTTTTTTAAATTGTGGGTCCCTATGCAGTATGCGACTGTTTTTGAGATGTTG
ACTTTGAGGTGAAAATCATTAATGAAAAGATAACAATTGGGAAAATTTCAAATTATTGGTCAGGATTTGCAAATAACATT
TTCACAAATACTGACAATTTTGTTATACATGTTCATGCAGATCTGCATATAAAATCAAAACAGCCATGATTAGAACCTGT
TTTCTCTTTGATTTTATGTTCTTTGAACATTCACTGACTGGGCTG

Alignment

ORF - retro_shar_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.86 %
• Parental protein coverage: 55.43 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TDNTGREVITVHRPLRCTSCWCPCYLQELEIQAPPGTIVGYVVQKWDPFLPKFTIQNE-SKEDILK-IVG
          T.NTG....TVHR.L.CTSCWC.C.L.ELEIQAPPGTI..YVV.K..P.L..FTI.N..SKE.....IVG
Retrocopy TNNTGQ*MFTVHR*LSCTSCWCLCHLKELEIQAPPGTILDYVV*K*EPSLTEFTI*NK<SKENMFF*IVG

Parental  PYATCGCFGDVDFEVKTINEKITIGKISKYWSGFVNDVFTNADNFGIHVPADLDV-KIKAAMIGACFLFD
          PYA.C.CF.DVDFEVK.INEKITIGKIS.YWSGF.N..FTN.DNF.IHV.ADL...KIK.AMI..CFLFD
Retrocopy PYAVCDCF*DVDFEVKIINEKITIGKISNYWSGFANNIFTNTDNFVIHVHADLHI<KIKTAMIRTCFLFD

Parental  FMFFEHSLAGL
          FMFFEHSL.GL
Retrocopy FMFFEHSLTGL

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_277 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	ENSSHAG00000017048	1 retrocopy	retro_shar_277 ,