RetrogeneDB ID: retro_shar_166

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834509.1:61187..61832(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000002850
• Aliases: None
• Description: None

Sequence

>retro_shar_166
TCATCACCAGTAAAAACTAAAGTAAAGACATGCCTTCCTGCTGATTGTACTTCAGGGGGCATCACTGTCACCCTGGATAA
TAATAGCATGTGGAATGAGTTCTATCATCGAAGCACAGAAATGATTCTAACTAAGCAGGGAAGACGCATGTTTCCTTATT
GTCGTTACTGGATAACTGGCTTAAATTCAAATTTGAAATATATCCTTGTAATGGACATTTCTCCTGTGGACAACCACCGC
TATAAATGGAATGGCCGCTGGTGGGAGCCCAGTGGTAAAGCAGAGCCTCATGTCTTGGGGAGGGTGTTCATTCATCCAGA
ATCTCCTTCTACCGGCCATTATTGGATGCATCAACCAGTGTCTTTCTATAAACTGAAACTTACCAACAATACACTCGATC
AGGAAGGGCACATTATCTTACATTCTATGCATCGTTACCTGCCACGGCTTCACCTGGTACCTGCAGAAAAGGCTACAGAA
ATTATACAGCTAAATGGTCCTGATGTCCATACTTTCACCTTCCCACAGACTGAGTTCTTTGCAGTGACAGCTTATCAGAA
CATTCAAATTACCCAGTTAAAAATAGATTACAACCCATTTGCCAAAGGGTTTCGGGATGATGGATTGAACAGCAAACCTC
AACGA

Alignment

ORF - retro_shar_166 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.09 %
• Parental protein coverage: 98.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSPAEPTTPRGPAASGAHGPITASLEDLELWTQFYQAGTEMVITKSGRRMFPQCKIRLSGLVPYLKYVVL
          SSP..........A....G.IT..L.....W..FY...TEM..TK.GRRMFP.C.....GL...LKY...
Retrocopy SSPVKTKVKTCLPADCTSGGITVTLDNNSMWNEFYHRSTEMILTKQGRRMFPYCRYWITGLNSNLKYILV

Parental  ADFVPMDNFRYKWTKDQWEVAGKAEPQLPGRSYVHPDSPAYGNHWMKEPVSFHKMKLTNNTLDQHGHIIL
          .D..P.DN.RYKW....WE..GKAEP...GR...HP.SP..G..WM..PVSF.K.KLTNNTLDQ.GHIIL
Retrocopy MDISPVDNHRYKWNGRWWEPSGKAEPHVLGRVFIHPESPSTGHYWMHQPVSFYKLKLTNNTLDQEGHIIL

Parental  HSMHRYQPRFLVVQAD---DLLNVCWSGFQVFSFPQTAFVSVTAYQNEQITKLKIDNNPFAKGFREQG--
          HSMHRY.PR...V.A................F.FPQT.F..VTAYQN.QIT.LKID.NPFAKGFR..G..
Retrocopy HSMHRYLPRLHLVPAEKATEIIQLNGPDVHTFTFPQTEFFAVTAYQNIQITQLKIDYNPFAKGFRDDGLN

Parental  KKPRR
          .KP.R
Retrocopy SKPQR

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_166 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	ENSSHAG00000002850	1 retrocopy	retro_shar_166 ,