RetrogeneDB ID: retro_shar_225

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834706.1:1632475..1633185(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSTA3
• Ensembl ID: ENSSHAG00000006859
• Aliases: None
• Description: tissue specific transplantation antigen P35B [Source:HGNC Symbol;Acc:12390]

Sequence

>retro_shar_225
AACCTGTACTTCTGGAGAAAGAACATTCAGATCAACACCAATGTTTTGCACTCAGCTTATGAGGTGGGCACCCAGAAGTG
ATCACTTGCCTCTACATCTGCATCTTCCCTGAGAAGACCACCTACCCCATCGATGAGACCATGATTCACAGTGGACCCCC
ACACAACAGCAACTTTGGCTGCTCCTATACTAAATGCATGATCAACATGAAAAATAGGGTATACTTCCAGCAATATGACT
GCACCTTCATTGCTGTCATCCCCACAAATGTCTTTGGACCCCTTGACAACTTCAACATTGAAGATAGCCATGTACTTCCT
GGCCTCATCCACAAAGTCTGCCTTGCAAAGAAGAAAGACTCTGCTCTGTCTGTGTGGGGCACTGGAAAGCCTCAAAGGCA
ATTCATCTAATCCTTGGACCTGGCTTGTCTCTCCCTCTGGGTCCCTTGAGAATACAATGAGGTAGAACCTATCATTCTAT
CAGTGGGTGAAGAGGATGAGGTGTCCATCAGGGAGGCAGCTGAAACCATCGTGGAGGCCATGAGCTTCCAAAGGGAACTG
AACTTTGACACAACCAAGGCAGATGGGCAGTTCAGGAATAGCAACAAGAAGTTAAGGACCTACTTTCCAGACTTTCAGTT
TATACCCTTCAAACAAGCTGTAAAGGAGACATGTGTCCAGTTTGAAAAAAACTATGAGCAAGCCAGGAAG

Alignment

ORF - retro_shar_225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 84.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLDFWRKNIQINDNVLHSAYEVGTRK-VISCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMID
          NL.FWRKNIQIN.NVLHSAYEVGT.K.VI.CL..CIFP.KTTYPIDETMIH.GPPHNSNFG.SY.K.MI.
Retrocopy NLYFWRKNIQINTNVLHSAYEVGTQK<VITCLYICIFPEKTTYPIDETMIHSGPPHNSNFGCSYTKCMIN

Parental  VQNRAYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVYLAKRNGSALTVWGTGKPRRQFIYSL
          ..NR.YFQQY.CTF.AVIPTNVFGP.DNFNIED.HVLPGLIHKV.LAK...SAL.VWGTGKP.RQFI.SL
Retrocopy MKNRVYFQQYDCTFIAVIPTNVFGPLDNFNIEDSHVLPGLIHKVCLAKKKDSALSVWGTGKPQRQFI*SL

Parental  DLARLFLWVLREYNEVEPIILSVGEEDEVSIREAAETIVEAMGFQGELNFDTTKADGQFKKTASNKKLRT
          DLA.L.LWV..EYNEVEPIILSVGEEDEVSIREAAETIVEAM.FQ.ELNFDTTKADGQF....SNKKLRT
Retrocopy DLACLSLWVP*EYNEVEPIILSVGEEDEVSIREAAETIVEAMSFQRELNFDTTKADGQFRN--SNKKLRT

Parental  YLPDFQFTPFKQAVKETCTWFENNYEQARK
          Y.PDFQF.PFKQAVKETC..FE.NYEQARK
Retrocopy YFPDFQFIPFKQAVKETCVQFEKNYEQARK

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_225 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
Callithrix jacchus	ENSCJAG00000021409	1 retrocopy	retro_cjac_1785,
Sarcophilus harrisii	ENSSHAG00000006859	1 retrocopy	retro_shar_225 ,