RetrogeneDB ID: retro_shar_110

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867574.1:421114..421831(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000008429
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000015376
• Aliases: None
• Description: None

Sequence

>retro_shar_110
TACCAGATGGTGGCCCAGTACCAGATCATGACCCGGTCCCGGGTAAGGGCAGCCCTGCGGGAGGCTGAAGCCAGCACTAG
TTCTCAGGCAATGGGGGCGGCCTTCACCAGGTCCAGGAGCAGAGAAACCCTGAGCGTGCAGGGGAGGAAGAAGCCCCGCT
CACGCAAGCGCATCCTCAAGGCCAAGCATCCCTCTCAGAACTACAGGGTAACTGATTATTTCCCCATCCGGAGGAGCACT
CGGAAGAATCGAGGTGAGCTGCGTAGCGAGGAGCGCATCAGACTCAATGCGTTGATTCAGAGTGGGAAGGAGGAGGGCAT
GCGAGTGGGGCTCTTTGAGGGGAAAGGTCGTGGAGTGATCACCACCAAGCCCTTCCAACGGGGTGACTACGTGGTGGAGT
ATCATGGGGATCTCATCGACTTGGCACTTGCCAAGAAGCGGGAGGCCCGCTACGCAAAAGACCCCGACACCGGTTGCTAC
ATGTACTACTTCCATTACCGAAGTAAAGGTTACTGCGTGGACGCCACCAAAGAGTCCGGCCGTCTGGGGCGTCTCATCAA
CCACAGCAAGAGTGGCAACTGCCAGACAAAGCTGCACCCCATCAATGGGGTGCCTCATCTTATCGTGATCGCCACCAGAG
ACATCGCAGTTGGTGAAGAGCTGCTCTATGACTACGGAGACCGAAGCAAGGCCTCCCTGGAGGCCTACCCCTGGCTG

Alignment

ORF - retro_shar_110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 62.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKPPKTKQASRRKAQGKTQQNRKVTDYYPVRRSSRKSKAELQSEEKRKLDELIESGKEEGMKIDIIDGKG
          KKP...K.....K......QN..VTDY.P.RRS.RK...EL.SEE...L..LI.SGKEEGM......GKG
Retrocopy KKPRSRKRILKAK---HPSQNYRVTDYFPIRRSTRKNRGELRSEERIRLNALIQSGKEEGMRVGLFEGKG

Parental  RGVIATKQFTRGEFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETDRLGRLI
          RGVI.TK.F.RG..VVEYHGDLI....AKKREA.YA.DP.TGCYMYYF.Y.SK.YCVDAT.E..RLGRLI
Retrocopy RGVITTKPFQRGDYVVEYHGDLIDLALAKKREARYAKDPDTGCYMYYFHYRSKGYCVDATKESGRLGRLI

Parental  NHSKCGNCQTKLHDIDGVPHLILIASRDIKAGEELLYDYGDRSKASLEAHPWL
          NHSK.GNCQTKLH.I.GVPHLI.IA.RDI..GEELLYDYGDRSKASLEA.PWL
Retrocopy NHSKSGNCQTKLHPINGVPHLIVIATRDIAVGEELLYDYGDRSKASLEAYPWL

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_110 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010371	1 retrocopy	retro_dnov_258,
Homo sapiens	ENSG00000183955	2 retrocopies	retro_hsap_2294, retro_hsap_4320,
Macaca mulatta	ENSMMUG00000013514	1 retrocopy	retro_mmul_1579,
Mus musculus	ENSMUSG00000049327	2 retrocopies	retro_mmus_1459, retro_mmus_3478,
Otolemur garnettii	ENSOGAG00000031093	1 retrocopy	retro_ogar_1217,
Pongo abelii	ENSPPYG00000005085	2 retrocopies	retro_pabe_1347, retro_pabe_1381,
Pan troglodytes	ENSPTRG00000005598	1 retrocopy	retro_ptro_1622,
Rattus norvegicus	ENSRNOG00000001062	4 retrocopies	retro_rnor_1551, retro_rnor_2837, retro_rnor_38, retro_rnor_679,
Sarcophilus harrisii	ENSSHAG00000015376	2 retrocopies	retro_shar_110 , retro_shar_115,
Tursiops truncatus	ENSTTRG00000015884	1 retrocopy	retro_ttru_1301,