RetrogeneDB ID: retro_shar_268

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL840156.1:314..950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000001232
• Aliases: None
• Description: None

Sequence

>retro_shar_268
AAAGCTCTTCCTCGAGTAACTCCTTTTTATGCTGTTAAATGTAATGACAGCAGAGCTATAGTGAAGATACTTGCTACTAT
AGGAGTAGGATTTGATTGTGCTAGCAAGACTGAAATACAATTAGTACAGAGCCTTGGGGTGCCTGCAGAGAGGATAATGT
GTGCAAATCCATGCAAACAAGTGTCACAATTTAAGTATGCTGCCAACAATGGAGTACAAATGATGACTTTTGATAGTGAA
GTAGAGCTAATGAAAGTTGCCAGAGTGCATCCAAAGGCAAAGCTTGTTTTAAGGATTGCCACTGATGACTCCAAAGCTGT
CTGTCAACTAAGTGTTAAATTTGGTGCCACTCTTAAAACTAGTAGGCTACTTCTTGAGCGAGCAAAGGAACTGAATGTTG
ATATTATTGGAGTTAGTTTCCACTTGGGAAGTGGTTGTACTGATCTAGAAACCTTTGTCCAAGCAGTTTCTGATGCCTAA
TGTGTCTTTGACATGGGGGTGGAGTTTGGTTTTAACATGTATCTTCTTGATATTGGTGGTGGCTTTCCTGGTTCTGAAGA
TATAAAGCTTAAGTTTGAAGAGATCTCAAGTGTAATCAATCTAGAATTAGACAAGTATTTTCCTTCTAACTCTGGG

Alignment

ORF - retro_shar_268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.83 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTLPRVTPFFAVKCNNSPSVLQVLANLGAGFDCASRGELEQVLKMGITPSRIIYANTCKQISYLQYAASH
          K.LPRVTPF.AVKCN.S......LA..G.GFDCAS..E...V...G....RI..AN.CKQ.S...YAA..
Retrocopy KALPRVTPFYAVKCNDSRAIVKILATIGVGFDCASKTEIQLVQSLGVPAERIMCANPCKQVSQFKYAANN

Parental  GIQLMTFDCEEELAKVAKFHPTARMVLRIWTEDSESMFPLSAKFGAPLDKCGHLLSIAKDLGVTVVGSAF
          G.Q.MTFD.E.EL.KVA..HP.A..VLRI.T.DS.....LS.KFGA.L.....LL..AK.L.V...G..F
Retrocopy GVQMMTFDSEVELMKVARVHPKAKLVLRIATDDSKAVCQLSVKFGATLKTSRLLLERAKELNVDIIGVSF

Parental  HVGSGCQTPESFHQAIANARRVFDLGLQMGHPMGFLDIGGGFPGQKNFVPTFEELAAVINRALDQYFPES
          H.GSGC...E.F.QA...A..VFD.G...G..M..LDIGGGFPG.......FEE...VIN..LD.YFP..
Retrocopy HLGSGCTDLETFVQAVSDA*CVFDMGVEFGFNMYLLDIGGGFPGSEDIKLKFEEISSVINLELDKYFPSN

Parental  SG
          SG
Retrocopy SG

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_268 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	ENSSHAG00000001232	1 retrocopy	retro_shar_268 ,