RetrogeneDB ID: retro_shar_391

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841579.1:70089..70469(+)
• Located in intron of: ENSSHAG00000000895

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN1
• Ensembl ID: ENSSHAG00000006382
• Aliases: None
• Description: stathmin 1 [Source:HGNC Symbol;Acc:6510]

Sequence

>retro_shar_391
CAGGTGAAAGAACTAAAGAAGCAAGCCTCAGGGCATGCTGCAGTCTCAGAATTCCCCTTTTCCCTTCCAAAGAAAAAAGA
TATTTCTCTGGAAGAAATTAAGAAGAAATGAGAAGCTGTACAAGAAAGACACAAGTTTTAAGAAGTTGAGATCTTGAAGT
AGCTAACTGAGTAGCAGAAACATGATGATATGGTTCAGAAATCAAGTGGAGAAAACAGCAATCTCAGTAAAATGGTAGAA
GGAAAAACTATAGCACAAAAGGAAGTCAAGAAAAAACCAAAAGGTACAAATAGCTGCTAAGCTAGCACACTTAAGGGAGA
CTGATAAGCTCATAGAGAGAAAGTACAGAAACACTGGAGTGCAAAGACCCTGCCAACAAG

Alignment

ORF - retro_shar_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.77 %
• Parental protein coverage: 71.11 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAFELILSPRSKEAVPEFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQLAEKREHEKEVLQKAI
          Q..EL........AV.EFP.S.PKKKD.SLEEI.KK.EA..ER.K..E.E.LK.L.E...H.....QK..
Retrocopy QVKELKKQASGHAAVSEFPFSLPKKKDISLEEIKKK*EAVQERHKF*EVEILK*LTE*QKHD-DMVQKSS

Parental  EENNNFSKMAE-EKLTHKMEANKENREAQMAAKLERLREKDKHMEEVRKNR-ESKDPADE
          .EN.N.SKM.E.EKL.HK....K.N...Q.AAKL..LRE.DK..E....N..E.KDPA..
Retrocopy GENSNLSKMVE>EKL*HKRKSRK-NQKVQIAAKLAHLRETDKLIERKYRNT>ECKDPANK

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_391 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855, retro_rnor_2048, retro_rnor_765,
Sarcophilus harrisii	ENSSHAG00000006382	1 retrocopy	retro_shar_391 ,