RetrogeneDB ID: retro_shar_23

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL869960.1:1026..2340(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000000441
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000008681
• Aliases: None
• Description: None

Sequence

>retro_shar_23
ATGACCATCTGCCACTTCTTCCTGCAGGGCCGCTGCCGCTTTGGGGAGCGCTGCTGGAACGAGCACCGGAGAGGGGGCAG
TGGCGGGGGTCGGCCTCTGCCGCAGCAGTACCCGGCGGCGCCCTCCGGTTGTAGCCGAGGGGGATGGAGCAACAGTTCTC
AGAGATATTCTAATGTCATCCAACCATCTAATTTCTCCAAATCCCCAACTTGGAGGGGCAGCAGAGATCCAAGGAAGACA
TCCTTTGGGTCCTTTGACTCAGGAGCTTCAAGTAGTGGAAGCAGAAATGTGGGGTTTTCTCAGAAGAGATTCTCTTCACT
GAACTCTAACCAAGTGGATGGGCAGAAAAATGAAGAGGATAAACTGACTGAAGGAATAGTAAAGGACATGGAAGTTTGGG
AATCTTCAGGGCAGTGGATGTTCTCTGTTTATTCACCAGTGAAAGAAAAGCCAAATATATCAGGTTTTACAGATATTTCA
CCAGAAGAGTTGAGACTTGAATACTCTAACTATATAAGCAGCAATAACTTACAAAGCTATCTGAATTCTATCCAGCAATT
AGTAAACCTGTGGAAGAGCAGGTTACTTGAACTGAAGAACATAAATTCAGCAACCAAAGGAGCATTGTTTTCTAAACTGA
AGAATGAAGGGGGACAAGTGGTTCCTCCTACCTTTGGATTTCAGAGTCAGCCAACCTCCACATTCGGTTCAGCAGCCTTC
CCAGGGAGCAGCAATAACAGCAGCAGCAGCAGTGTCCAGAATTTCAGTTTTAAGCCCACTTTGGGATTTGGGGCCACCCC
GTCAGGCAGCAGCACCTCTGTCTTTGGCTCACCGGCCTCCCTGGCACTCACGGCTGCATCTTCCTCCGGCTCGACAATGA
CCTCCTCCACTCCCACTTCCTTTGGGTTCGGGGAGTCCTCCACTGTCTCGGCAGCATCTTTTTCATTCAAAAGCCCGGAA
GTTTTTAGCTTTGGATCAGCTGGGTTTTCAGGATTTCCTGCTTCTTCCCCATTAAGCACAGCAGGTGCCACCAGCACCCC
TGCTTTTGGGGGAGAGGGTGGCGCAACAGGGTGGGGTGGCTTCGGCCCCTCGGGCTCGGGGGCCAACTTGTTTGGACTGC
CCACCAGCGGCTTTGGGCCCGGTGGCCCCTCCTCCTCCTCTGAGCCGCCGACCGGGGCTGGTAACACGGCCGAGAACCTG
TTCACACCCAAGAACGAACTGACAGCCGAGGAGCTCAAACAGTTTGTGGCAAAGAAGTTTACATTAGGGAAGGTTCCCCT
CAAGCCACCACCAGAAGGGCTTCTGAGCCTTTAA

Alignment

ORF - retro_shar_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCSRGGWSNSSQRYSNVIQPSNFSKSTTWGGSRDPGKTSFGSFDSGASSSGSRNVGFSQNRFSSLNSNQV
          GCSRGGWSNSSQRYSNVIQPSNFSKS.TW.GSRDP.KTSFGSFDSGASSSGSRNVGFSQ.RFSSLNSNQV
Retrocopy GCSRGGWSNSSQRYSNVIQPSNFSKSPTWRGSRDPRKTSFGSFDSGASSSGSRNVGFSQKRFSSLNSNQV

Parental  DGQKDEEDKLIEGIVKDMEVWESSGQWMFSVYSPVKEKPNISGFTDISPEELRLEYSNYISSNNLQSYLN
          DGQK.EEDKL.EGIVKDMEVWESSGQWMFSVYSPVKEKPNISGFTDISPEELRLEYSNYISSNNLQSYLN
Retrocopy DGQKNEEDKLTEGIVKDMEVWESSGQWMFSVYSPVKEKPNISGFTDISPEELRLEYSNYISSNNLQSYLN

Parental  SIQQLVNLWKSRLLELKNINSATKGALFSKLKNEGGQVVP-TFGFQSQPTSTFGSAAFPGSSNNSSSSSV
          SIQQLVNLWKSRLLELKNINSATKGALFSKLKNEGGQVVP.TFGFQSQPTSTFGSAAFPGSSNNSSSSSV
Retrocopy SIQQLVNLWKSRLLELKNINSATKGALFSKLKNEGGQVVPPTFGFQSQPTSTFGSAAFPGSSNNSSSSSV

Parental  QNFSFKPTSGFGAAPSGSSTSVFGSPASPALTAASSSGSTMTSSAPTSFGFGESSTVSAASFSFKSPEVF
          QNFSFKPT.GFGA.PSGSSTSVFGSPAS.ALTAASSSGSTMTSS.PTSFGFGESSTVSAASFSFKSPEVF
Retrocopy QNFSFKPTLGFGATPSGSSTSVFGSPASLALTAASSSGSTMTSSTPTSFGFGESSTVSAASFSFKSPEVF

Parental  SFGSAGFSGFPASSPLSTAGATSTPAFGGGGGATGGGGFGPSGSGANLFGLPTSGFGPGGPSSSSSSGPP
          SFGSAGFSGFPASSPLSTAGATSTPAFGG.GGATG.GGFGPSGSGANLFGLPTSGFGPGGPSSSS...PP
Retrocopy SFGSAGFSGFPASSPLSTAGATSTPAFGGEGGATGWGGFGPSGSGANLFGLPTSGFGPGGPSSSSE--PP

Parental  SGAGNTAENLFTPKNELTAEELKQFVAKKFTLGKVPLKPPPEGLLSV
          .GAGNTAENLFTPKNELTAEELKQFVAKKFTLGKVPLKPPPEGLLS.
Retrocopy TGAGNTAENLFTPKNELTAEELKQFVAKKFTLGKVPLKPPPEGLLSL

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_23 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000008681	1 retrocopy	retro_shar_23 ,