RetrogeneDB ID: retro_shar_684

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL857013.1:1193266..1194002(-)
• 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_684
TCCAGATCCAAGTCGAGGTCCAGGTTTGAGTCTCGATCGAGATCCAGAAGAAGTTCTCGAAGGCATTATACTAGATCACG
TTCTCGCTCCCGCTCCCACAGACGATCCCGGAGCAGGTCGTACAGTCGAGATTACCGAAGGCGACATAGCCACAGTCACT
CTCCAAAGTCTACCCGCAGGTGTCACGTTGGGAATAGAGCCAATCCCGACCCCAATTGTTGTCTCGGAGTGTTTGGATTG
AGTTTGTATACTAATGAGAGGGATCTCAGAGAAGTATTTTCCAAATATGGCCCAATTGCGGATGTGTCCATTGTGTATGA
CCAACAGTCTCGGCGCTCCCGAGGATTTGCCTTTGTCTACTTTGAGAATGTGGATGATGCCAAGGAAGCTAAAGAGCGTG
CCAATGGAATGGAACTGGATGGCCGGAGGGTCCGAGTAGACTTTTCTATAACAAAAAGACCCCACACCCCAACCCCTGGA
ATCTACATGGGAAGACCTACTTATGGCAGTTCCCGCCGTCGTGGTTACTATGATAGAGGCTACAATCGAGGGTATGATGA
TCGTGATTATTACAGCAGATCTTACAGAGGAGAAGGTGGAGGAGGAGGAGGGTGGAGAGCTGCCCAAGACAGGGATCAGA
TTTACAGGAGGCCATCACCCTCCCCATATTACAGTCGTGGGGGTTATAGGTCATGGTCTTGATCTCGATTTTATTCACCT
TGTGGCTATTAGAGCA

Alignment

ORF - retro_shar_684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.5 %
• Parental protein coverage: 88.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRSKSRSRSESRSRSRRSSRRHYTRSRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPD
          SRSKSRSR.ESRSRSRRSSRRHYTRSRSRSRSHRRSRSRSYSRDYRRRHSHSHSP.STRR.HVGNRANPD
Retrocopy SRSKSRSRFESRSRSRRSSRRHYTRSRSRSRSHRRSRSRSYSRDYRRRHSHSHSPKSTRRCHVGNRANPD

Parental  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEKNGSAKKAKERANGMELD
          PNCCLGVFGLSLYT.ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE....AK.AKERANGMELD
Retrocopy PNCCLGVFGLSLYTNERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD

Parental  GRRIRVDFSITKRPHTPTPGIYMGRPTYGSSRRRDYYDRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQD
          GRR.RVDFSITKRPHTPTPGIYMGRPTYGSSRRR.YYDRGY.RGYDDRDYYSRSYRG.GGGGGGWRAAQD
Retrocopy GRRVRVDFSITKRPHTPTPGIYMGRPTYGSSRRRGYYDRGYNRGYDDRDYYSRSYRGEGGGGGGWRAAQD

Parental  RDQIYRRRSPSPYYSRGTGH-GLGLDL--IHLVAIKA
          RDQIYRR.SPSPYYSRG.G..G.GLDL..IHLVAI.A
Retrocopy RDQIYRRPSPSPYYSRG-GY>GHGLDLDFIHLVAIRA

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_684 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,