RetrogeneDB ID: retro_shar_55

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL848859.1:726..2265(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000000383
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000010846
• Aliases: None
• Description: None

Sequence

>retro_shar_55
ATGACGACCTTGGGGACCAGCAGTCAGACTGTGACTGAATATGTTGTTCGAGTTCCAAAGAACAACCTCAAGAGGTACAA
TATCGTGGCTTTTAATGCCGCTGACAAAGTCAACTTCTCCACTTGGCATCAGGCCAAGATGAAACGGGATCTGAGCAGCA
AGAAGCTCTATCAGGAGGAAGAGATGCCAGAATCTGGGGCTGGCAGTGAGTTTAATCGGAAGCTCCGGGATGAGGCCAGG
AGCAAGCATGGCCTTCTCAAAACCTTCAAGGCTGAAGACCAGCCCTGGCTACTCAAAGTCAATGGCAAAACAGGCAGAAG
GTTCAAGGGAATGAAGAGGAGTGGGGTGACAGAAAACGCCTCGTACTACATCTTCATCCAGTGCCCCGACGGGGTCTTCG
AAGCCTTCCCCGTGCACAGCTGGTACAACTTCACTCCTCTGGCGCGGCACCGGACACTCACGGCCGAGGAGGCTGAGGAG
GAATGGGAAAAGAGGAACAAAGTCCTGAACCACTTCAGCATCATGCAACAGCGGCGGCTGAAGGATCAGGACCACAGTGA
GGATGAAGATGAGCATAAAGAGAAGAGCCGGAAGAAGCCCAGTGAGCTCCGCATCCACGACCTGGAGATGAGCTCTGATG
ACAGCAATAGCAGTGGGGAGGAAGGAGAAAAGGTCCCCAAGAGCAAGAAGAAGGCAGGTCCCTCCAGGGGGGGCAAGAAG
AAGAAAAAGGGCTCTGATGATGAGGCCTTTGAGGACAGCGATGATGGGGACTTTGAGGGCCATGAGGTGGACTACATGTC
AGATGGCTCCAGCAGTTCTGAGGAGGAGGCAGTAGGGAAAGCCAAAGTGGTCCGGCAGGAGGAGGATGGCCCTAAAGGTA
TTGATGAGGAAAGTGAAAGCAGTGAGGAGAGTGAGGAGGAGAAGCCCCCCGAGGAGGAGGAGAAGAAGGAAGAAGATAAG
AAGGCCCCCAACCCGCAGAAGAGGAGGAGGAAAGGAGACAGGAGCGAGGAGTCAGACAACTCCGAGGAGAGCGACATCGA
CAACAAGGTGACCTCGGTCCTCTTCATGACCAAGAAGAAGACCCCCCCAAAGGGAGAGCGGAAGGCCTCAGGCAGCAGCT
CCAGGGGCAACAGCCGCCCGAGCACTCCCAGCTTGGACAGCGGCAGTACGTCCTCCACCCTGCGGGCAGCCTCTAGCAAG
CTGGGGCAAGGGAAGCCGCAGACAGAACCCAGTGATACTCCCCCCGCCAAGCGCCTGAGGCTGGATGCCGGGCCCCAGAG
CATCGCTACGAAATCCACCCCCCAGCCTCAGTCCGACAAGTCCATGTCCAGCAGTGATGATGTGCAGGTGATAGAATGCA
AAGTCAGGCGCTACCTGATCCAAAAGCCCATGACCGCCAAGGACCTGATGAAGAAGTTCCAGACCAAAAATACAGGGCTC
AGCAGCCACCAGACAGTCAACATGCTGGCCCAGATCTTGAAACGCCTCAAACCGGAGCGCAAGATGATCGATGACAAGAT
GCACTTCTTCCTTAAGGAA

Alignment

ORF - retro_shar_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAKMERDLSNKKIYQEEEMPESGAGSEFNRKLRDEARRKKYGIILKTFKAEDQPWLLKVNGKTGRRFKGV
          QAKM.RDLS.KK.YQEEEMPESGAGSEFNRKLRDEAR..K.G..LKTFKAEDQPWLLKVNGKTGRRFKG.
Retrocopy QAKMKRDLSSKKLYQEEEMPESGAGSEFNRKLRDEAR-SKHGL-LKTFKAEDQPWLLKVNGKTGRRFKGM

Parental  KKGGVTENTSYYIFTQCPDGAFEAFPVHNWYNFTPLARHRTLTAEEAEEEWERRNKVLNHFSIMQQRRLK
          K..GVTEN.SYYIF.QCPDG.FEAFPVH.WYNFTPLARHRTLTAEEAEEEWE.RNKVLNHFSIMQQRRLK
Retrocopy KRSGVTENASYYIFIQCPDGVFEAFPVHSWYNFTPLARHRTLTAEEAEEEWEKRNKVLNHFSIMQQRRLK

Parental  DQDHDEDEDEHKEKKNRKKPSELRIHDLEDDLEMSSDDSNSSGEEGEKVPKSKKKAAPSRGGKKKKKKGS
          DQDH.EDEDEHKE.K.RKKPSELRIHDLE....MSSDDSNSSGEEGEKVPKSKKKA.PSRGG.KKKKKGS
Retrocopy DQDHSEDEDEHKE-KSRKKPSELRIHDLE----MSSDDSNSSGEEGEKVPKSKKKAGPSRGG-KKKKKGS

Parental  DDEAFEDSDDGDFEGQEVDYMSDGSSSSEEEAVGKAKVVQQEEDGPKGIDEESESSEESEEEKPPEEEEK
          DDEAFEDSDDGDFEG.EVDYMSDGSSSSEEEAVGKAKVV.QEEDGPKGIDEESESSEESEEEKPPEEEEK
Retrocopy DDEAFEDSDDGDFEGHEVDYMSDGSSSSEEEAVGKAKVVRQEEDGPKGIDEESESSEESEEEKPPEEEEK

Parental  EEEDKKAPNPQEKKKRKGDSSEESDTSEESDIDNEASSALFMTKKKTPPKREQKASGNSSRGNSRPSTPS
          .EEDKKAPNPQ.K..RKGD.SEESD.SEESDIDN...S.LFMTKKKTPPK.E.KASG.SSRGNSRPSTPS
Retrocopy KEEDKKAPNPQ-KRRRKGDRSEESDNSEESDIDNKVTSVLFMTKKKTPPKGERKASGSSSRGNSRPSTPS

Parental  VDSGSTSSTLRAAASKLEQGKRQTGPSDTPAAKRLRLDAGPQSISGKSTPQPQSGKSTPSSGDVQVTEDA
          .DSGSTSSTLRAA.SKL.QGK.QT.PSDTP.AKRLRLDAGPQSI..KSTPQPQS.KS..SS.DVQV.E..
Retrocopy LDSGSTSSTLRAASSKLGQGKPQTEPSDTPPAKRLRLDAGPQSIATKSTPQPQSDKSMSSSDDVQVIECK

Parental  VRRYLTRKPMTTKDLLKKFQTKKTGLSSDQTVNVLAQILKRLNPERKMINDKMHFSLKE
          VRRYL..KPMT.KDL.KKFQTK.TGLSS.QTVN.LAQILKRL.PERKMI.DKMHF.LKE
Retrocopy VRRYLIQKPMTAKDLMKKFQTKNTGLSSHQTVNMLAQILKRLKPERKMIDDKMHFFLKE

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_55 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
Macaca mulatta	ENSMMUG00000007904	1 retrocopy	retro_mmul_689,
Sarcophilus harrisii	ENSSHAG00000010846	1 retrocopy	retro_shar_55 ,