RetrogeneDB ID: retro_shar_826

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867596.1:170739..171330(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2B
• Ensembl ID: ENSSHAG00000002437
• Aliases: None
• Description: transformer 2 beta homolog (Drosophila) [Source:HGNC Symbol;Acc:10781]

Sequence

>retro_shar_826
CAATCCCGGAGCAGGTCTTACGGTCGAGATTACCGTGAATACCGAAGACGGCGCCCTAGCCATTCTCCTCTGGCTACTCG
CAGGCGTCATCTGGGAAATCGGTCCAATCCCGATCCCAATTGTTGTCTCGGCGTATTCGGTTTGAGCCTGTACACCACCG
AAAGGGATCTAAGACAAATATTCACCAAATATGGCCCGATTTCTCACGTCTCCATTGTTTATGACCAACAATCTAGGCGC
TCACGGGGGTTTGCTTTTGTGTATTTTGAAAACGTGGAAGAAGCTAAGAAAGCTAAAGAGAGGGTCGATGGAATAGAGCT
TGACGGAAGAAGGATCAGAGTGGATTTTTCTATTACAAAAAGACCCCACACACCTACACCTGGAATCTACATGGGAAGAC
CTACTTACAACAGACGTCGTGACTACCACGAAAGGCCATATGATCGCGGATATGAGAGGGATTATTATAATAGATCCTAT
AGAGGAGTAAGTGGAGGAATATCTGGGGGAGGTGGGGGAAGCTGGAGAAGCGTTCAAGATAGGGAGGTAGTTTACAGACG
GCGAACACCATCACCCCGTTACAGCCGTGGG

Alignment

ORF - retro_shar_826 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.0 %
• Parental protein coverage: 69.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSRSRSYSRDYR--RRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADV
          .SRSRSY.RDYR..RR...SHSP..TRRRH.GNR.NPDPNCCLGVFGLSLYTTERDLR..F.KYGPI..V
Retrocopy QSRSRSYGRDYREYRRRRPSHSPLATRRRHLGNRSNPDPNCCLGVFGLSLYTTERDLRQIFTKYGPISHV

Parental  SIVYDQQSRRSRGFAFVYFEKNGSAKKAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGRPTYGSSR
          SIVYDQQSRRSRGFAFVYFE....AKKAKER..G.ELDGRRIRVDFSITKRPHTPTPGIYMGRPTY...R
Retrocopy SIVYDQQSRRSRGFAFVYFENVEEAKKAKERVDGIELDGRRIRVDFSITKRPHTPTPGIYMGRPTY--NR

Parental  RRDYYDRGYDRGYDDRDYYSRSYRGGGGG----GGG-WRAAQDRDQIYRRRSPSPYYSRG
          RRDY..R.YDRGY..RDYY.RSYRG..GG....GGG.WR..QDR...YRRR.PSP.YSRG
Retrocopy RRDYHERPYDRGY-ERDYYNRSYRGVSGGISGGGGGSWRSVQDREVVYRRRTPSPRYSRG

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_826 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Sarcophilus harrisii	ENSSHAG00000002437	2 retrocopies	retro_shar_684, retro_shar_826 ,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,