RetrogeneDB ID: retro_shar_59

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841386.1:2284892..2286179(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000016675
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000007189
• Aliases: None
• Description: None

Sequence

>retro_shar_59
ATGGCTTCCTCAGATGTGGCGCGGCATATGGTCTATCAGTCTCTTGTGGGAATCAAAGCAACTTGTGTCTCCTCCCAACC
ATGCAAGGAAGAAAAAATATCAGACGATAGCCCTCGTTGTTTAACTATGACTGGCTATGTGGGTTTTGAAAGTTTGCCTG
ATCAGTTGGTCAGCAAGACCCTTCAGCAAGGGTTCTGTTTTAACATTCTCTGTGTGGGGGAAACTGGAATCGGAAAGTCA
ACCCTGATAGACACATTGTTTAACACTAATTTTGATAACTCTGTATCCTCACACTTTCACCCAAATGTAAGACTTAAAGC
CCAGACATATGAACTACAGGAAAGCAATGTCCGATTGAAACTGACCATCGTAAATACAGTGGGATTTGGAGACCAGATAA
ATAAAGAAGATAGCTATCGACCAATAGTGGATTACATAGATGCTCAATTTGAGGCTTATCTCCAAGAAGAATTGAAGATT
AAACGTTCACTCTTTAACTACCGAGATTCTCGAATTCATGTCTGCCTTTATTTTATTTCACCTACAGGCCATTCCCTTAA
GCGCCTTGACTTGTTAACCCTGAAGAAACTGGACAGGAGGGTAAATATCATCCCTGTGATTGCCAAAGCAGACACAATTA
CTAAATGTGAATTGCAGAGGTTTAAACTTAGACTCATGAGTGAATTGGTCACCAATGGAATCCAAATATACCAATTCCCA
ACAGATGATGAAACTGTTGCTCATCTTAATGCTTCAATGAATGGACACTTGCCATTTGCTGTGGTGGGTAGTACAGAGGA
GATCAAACTGGGAAATAAGATGGTGAAAGCTCGTCAGTACCCATGGGGCATTGTGCAAGTGGAAAATGAAAATCACTGTG
ACTTTGTAAAGCTCCGCGAAATGCTCATTTGCACAAATATGGAAGACCTGAGAGAACAAACCCATGTTCTACACTATGAA
AATTATAGACGTTGCAAACTGGAGGAAACAGGTTTTAAAGATGTAAACCTAGAGAAAAAACCTGTAAGTGTGCAGGAGGC
ATATGAAATCAAAAGGTACGAATCCTTTGGCGAACTTCAAAGAAAAGAAGAAGAGATGAAACAGTTGTTTGTAAAGCGAG
TGAAAGAGAAAGAAGCTATTTTGAAAGAAGCTGAACGAGAGCTTCAGGCAAAATTTGAACACCTTAAAAGACTTAATCAA
GAAGAAAGAATGAAACTTGAAGAAAAGAGAAGAGCTTTAGAAGAGGAAATAAATGCTCTTGGTAAAAGGAAAGCTGCATG
TGAACTA

Alignment

ORF - retro_shar_59 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.92 %
• Parental protein coverage: 94.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSSDVARHPIYQSLGGMK-TCSTSQSSKEE---DDTPRCLNITGHVGFESLPDQLVNRSIQQGFCFNIL
          M.SSDVARH..YQSL.G.K.TC..SQ..KEE...DD.PRCL..TG.VGFESLPDQLV....QQGFCFNIL
Retrocopy MASSDVARHMVYQSLVGIKATCVSSQPCKEEKISDDSPRCLTMTGYVGFESLPDQLVSKTLQQGFCFNIL

Parental  CVGETGIGKSTLIDTLFNTNFDDLESSHFHPNVRLKAQTYELQESSVRLKLTIVNTVGFGDQINKEESYQ
          CVGETGIGKSTLIDTLFNTNFD...SSHFHPNVRLKAQTYELQES.VRLKLTIVNTVGFGDQINKE.SY.
Retrocopy CVGETGIGKSTLIDTLFNTNFDNSVSSHFHPNVRLKAQTYELQESNVRLKLTIVNTVGFGDQINKEDSYR

Parental  PIVDYIDAQFEAYLQEELKIKRSLFNYHDSRIHACLYFISPTGHSLKTLDLLTMKSLDSKVNIIPVIAKA
          PIVDYIDAQFEAYLQEELKIKRSLFNY.DSRIH.CLYFISPTGHSLK.LDLLT.K.LD..VNIIPVIAKA
Retrocopy PIVDYIDAQFEAYLQEELKIKRSLFNYRDSRIHVCLYFISPTGHSLKRLDLLTLKKLDRRVNIIPVIAKA

Parental  DTISKTELQKFKIKLMSELVSNGVQIYQFPTDDETISQINSSMNGHLPFAVVGSMEEVKLGNKMVKARQY
          DTI.K.ELQ.FK..LMSELV.NG.QIYQFPTDDET....N.SMNGHLPFAVVGS.EE.KLGNKMVKARQY
Retrocopy DTITKCELQRFKLRLMSELVTNGIQIYQFPTDDETVAHLNASMNGHLPFAVVGSTEEIKLGNKMVKARQY

Parental  PWGIVQVENENHCDFVKLREMLICTNMEDLREQTHTRHYELYRRCKLEEMGFKDVSPENKPVSLQEAYEI
          PWGIVQVENENHCDFVKLREMLICTNMEDLREQTH..HYE.YRRCKLEE.GFKDV..E.KPVS.QEAYEI
Retrocopy PWGIVQVENENHCDFVKLREMLICTNMEDLREQTHVLHYENYRRCKLEETGFKDVNLEKKPVSVQEAYEI

Parental  KRHEFYGERQRKEEEMKQMFVQRVKEKEAILKEAERELQAKFEHLKRLHQEERMKLEEKRRYLDEEISAF
          KR.E..GE.QRKEEEMKQ.FV.RVKEKEAILKEAERELQAKFEHLKRL.QEERMKLEEKRR.L.EEI.A.
Retrocopy KRYESFGELQRKEEEMKQLFVKRVKEKEAILKEAERELQAKFEHLKRLNQEERMKLEEKRRALEEEINAL

Parental  AKRKAASEL
          .KRKAA.EL
Retrocopy GKRKAACEL

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_59 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009949	1 retrocopy	retro_chof_2159,
Monodelphis domestica	ENSMODG00000003104	1 retrocopy	retro_mdom_93,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258,
Sarcophilus harrisii	ENSSHAG00000007189	1 retrocopy	retro_shar_59 ,