RetrogeneDB ID: retro_shar_20

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856734.1:2301619..2303185(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000016708
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000004229
• Aliases: None
• Description: None

Sequence

>retro_shar_20
ATGGCCAAAGGCGAGGGCGCAGAGAGCGGCTCAGCCACCGGGCTGCTCTCCCCGGGCATCCTCCGGGGTGAGGAGAACCG
TCGGACCCAGAAAGGTGGGAAGAAACAACTGAGCATCTGCAGAAAGCTCTGCTATGCTGTAGGGGGTGCTCCCTACCAGA
TCACTAGCTGCACCCTGGGCTTCTTCCTTCAGATCTTCCTGCTGGATGTGGCTCAGGTGGGCCCCTTCTCTGCTTCCATC
ATTCTGTTTGTGGGCCGTGTCTGGGACGCCATCACTGACCCCTTGGTAGGATTTTGCATCAGCAAATCTTCCTGGAGCCG
TCTGGGCCGTCTAATGCCCTGGATAATCTTCTGCACGCCACTGGCTGTGATCGCCTATTTTCTCATCTGGTTCGTTCCTG
ACTTTTCCAGTAATCAGGTTTGGTGGTACCTGATCTTCTATTGCCTGTTTGAGACGCTGGAGACGTGTTTCCACGTTCCA
TACTCGGCCCTCACCATGTTTATCAGCACAGAACAGAGCGAACGTGACTCGGTCACAGCATACCGGATGACTGCAGAAGT
GCTGGGTACAGTGCTGGGCGCTGCCATTCAGGGGCAAATTGTGGGCAAAGTGGACACTCCCTGTATTCCAGATCCTGACA
TACTTGTGGAGAAGGTGAATCGGACACATGCTACCAGCTCCCTGAATGATACGAAGAATGCCTACATGCTGGCTGCGGGA
GTCATCGCCTCCATCTACGTTCTCTGTGCGGTCATCTTGTCTCTGGGGTTGCAGGAGCACAGAGAGCCCTGTGAGAAGAA
GGAGCAGCCGCCTTCTTTTTTCCAAGGGCTCCGACTGGTCATGAGCCATGGCCCTTATATCAAACTCATTGCCGGCTTCT
TGTTCATCTCTCTGGCTTTCATGCTGGTAGAAGGAAACTTTGCTTTGTTCTGCACCTACACCCTGGACTTCCGGAACGAG
TTTCAGAATCTGCTCCTGGCCATCATGCTCTCGGCCACTCTTACCATACCCATCTGGCAGTGGTTCCTGACCCAGTTTGG
CAAGAAGACGGCTGTGTATGTGGGGATCTTGTCAGTTGTCCCCTTCCTCATCTTAGTTGCCCTGATGGAGAGTAACCTGA
TCGTCACCTATGTGGTGGCCGTGGCTGCAGGGGTCAGCGTGGCCGCTGCCTTCCTCCTGCCTTGGTCTATGCTGCCCGAC
GTGATTGATGACTTCCATCTAAAGCAGCCCAACGCCAGGGGACACGAACCCATCTTCTTCTCCTTCTACGTCTTCTTCAC
CAAATTTGCCTCCGGTGTCTCCCTGGGCATCTCTACTCTCAGCCTCAACTTTGCAGGTTATTTGACAAGGGGCTGCTCCC
AGCCCGAAACGGTCAAGTTCACTTTGAAGATTCTGGTGACTGTTGTCCCCATCGGCCTCATCCTTTTGGGTCTGTTTGTC
TTCAGGCTGTATCCTATTGATGAAGAAAAACGTCGGGAAAACAAGAAAGCCCTGCAGGTGATCAGGGAAGAAGCAGGAAG
CGCCGGCTCTGACACGGACTCTACAGAACTGATCACCATCCTCTAG

Alignment

ORF - retro_shar_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKGEGAESGSATGLLSPGILRGEETRRTQKGGKKQLTICSKLCYAVGGAPYQITGCALGFFLQIYLLDV
          MAKGEGAESGSATGLLSPGILRGEE.RRTQKGGKKQL.IC.KLCYAVGGAPYQIT.C.LGFFLQI.LLDV
Retrocopy MAKGEGAESGSATGLLSPGILRGEENRRTQKGGKKQLSICRKLCYAVGGAPYQITSCTLGFFLQIFLLDV

Parental  AQVDPFSASIILFVGRAWDAITDPLVGFCISKSSWSRLGRLMPWIIFSTPLAVIAYFLIWFVPDFSRNQA
          AQV.PFSASIILFVGR.WDAITDPLVGFCISKSSWSRLGRLMPWIIF.TPLAVIAYFLIWFVPDFS.NQ.
Retrocopy AQVGPFSASIILFVGRVWDAITDPLVGFCISKSSWSRLGRLMPWIIFCTPLAVIAYFLIWFVPDFSSNQV

Parental  LWYLVFYCLFETLVTCFHVPYSALTMFISTEQSERDSATAYRMTVEVLGTVLGTAIQGQIVGKVDTPCIQ
          .WYL.FYCLFETL.TCFHVPYSALTMFISTEQSERDS.TAYRMT.EVLGTVLG.AIQGQIVGKVDTPCI.
Retrocopy WWYLIFYCLFETLETCFHVPYSALTMFISTEQSERDSVTAYRMTAEVLGTVLGAAIQGQIVGKVDTPCIP

Parental  DPDILVEEVNQTHDTSSLNDTKNAYMLAAGVIASIYVLCAVILSLGVQEHREPCEKKEQPPSFFRGLRLV
          DPDILVE.VN.TH.TSSLNDTKNAYMLAAGVIASIYVLCAVILSLG.QEHREPCEKKEQPPSFF.GLRLV
Retrocopy DPDILVEKVNRTHATSSLNDTKNAYMLAAGVIASIYVLCAVILSLGLQEHREPCEKKEQPPSFFQGLRLV

Parental  MNHGPYIKLIAGFLFTSLAFMLVEGNFALFCTYTLGFRNEFQNLLLAIMLSATLTIPIWQWFLTRFGKKM
          M.HGPYIKLIAGFLF.SLAFMLVEGNFALFCTYTL.FRNEFQNLLLAIMLSATLTIPIWQWFLT.FGKK.
Retrocopy MSHGPYIKLIAGFLFISLAFMLVEGNFALFCTYTLDFRNEFQNLLLAIMLSATLTIPIWQWFLTQFGKKT

Parental  AVYVGISSAVPFLILVALMESNLIVTYVVAVAAGVSVAAAFLLPWSMLPDVIDDFHLKQPNARGHEPIFF
          AVYVGI.S.VPFLILVALMESNLIVTYVVAVAAGVSVAAAFLLPWSMLPDVIDDFHLKQPNARGHEPIFF
Retrocopy AVYVGILSVVPFLILVALMESNLIVTYVVAVAAGVSVAAAFLLPWSMLPDVIDDFHLKQPNARGHEPIFF

Parental  SFYVFFTKFASGVSLGISTLSLDFAGYLTRGCSQPEAVKFTLKILVTVVPIGLILLGLFVFKLYPIDEEK
          SFYVFFTKFASGVSLGISTLSL.FAGYLTRGCSQPE.VKFTLKILVTVVPIGLILLGLFVF.LYPIDEEK
Retrocopy SFYVFFTKFASGVSLGISTLSLNFAGYLTRGCSQPETVKFTLKILVTVVPIGLILLGLFVFRLYPIDEEK

Parental  RRENKKALQVIREEAGSSGSDTDSTELASIL
          RRENKKALQVIREEAGS.GSDTDSTEL..IL
Retrocopy RRENKKALQVIREEAGSAGSDTDSTELITIL

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_20 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000004229	1 retrocopy	retro_shar_20 ,