RetrogeneDB ID: retro_shar_121

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861653.1:738146..738935(+)
• Located in intron of: ENSSHAG00000008019

Retrocopy information

• Ensembl ID: ENSSHAG00000010737
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000008895
• Aliases: None
• Description: None

Sequence

>retro_shar_121
CAAGATCCTCTCGTTTGGGGATATGGCAGGAACAATGGACCAGATAGCTGGCATAAGCTTTTTCCTATCGCCAATGGAAG
GCGTCAGTCCCCTATTGATATTAAGCTCTGGAGCGCCAAGTTTGACAGCTCCCTGAAACCTCTGAATTTTAACTACGATT
CTTCAACAGCTCAAGGGATTGTCAACAAGGGTTATTCTTTCAATGTAGAGTTCGATGATTCTAGTGACAAATCGGTGCTA
AGCGGAGGACCTCTAACTGAGAGATACAGATTGGCTCACTTCAGTTTTCACTGGGGTTGCAGGGATGATCAAGGCTCAGA
GCACAGTATTGATGACCTGAAATATGCAGCGGAGCTCCACTTGGTTCACTGGAATACAAAATACAAGACGTTCTGCGATG
CGCTGCACCATTCTGATGGACTAGCTATAGTGGGTGTTTTTTTGACAATAGGAAATTCTGAGCCTGAACTACAGGAAGTC
ATCGATGCATTAGATGCCATTAAACAAAGAAATATGCATGCTGTTTTTACAGACTTCAATCCAGCTTGCCTTCTTCCTGA
TAACCTCGACTTTTGGACTTACTCAGGCTCCCTGACCATTCCTCCTCTTTTAGAATGTGTGGTTTGGATCGTCTTACGGG
AGCCCATTAATATCACCAAAGAACAGCTATCTAAATTTCGAAGTCTTTACTCCACTACTAAGGGAGAATATCCCCAGAGG
CACATGGTGGAAAACTGGCGCCCATGTCAGCCTCTGCAGGGCAGACAGGTTAGAAGGTTCTTAAAATAA

Alignment

ORF - retro_shar_121 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.37 %
• Parental protein coverage: 97.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WGYEPGVNGPEKWHEAFPIARGKRQSPVEIELSKTLYDSSLKPLHITYDPCDAKRIINNGHSFNVEFDDS
          WGY....NGP..WH..FPIA.G.RQSP..I.L.....DSSLKPL...YD...A..I.N.G.SFNVEFDDS
Retrocopy WGYGRN-NGPDSWHKLFPIANGRRQSPIDIKLWSAKFDSSLKPLNFNYDSSTAQGIVNKGYSFNVEFDDS

Parental  TDTSVLCGGPLIGKYRLIQFHFHWGSSTNVEGSEHILDGKQYAAELHLVHWNTKYESFKVAVTKDDGLAV
          .D.SVL.GGPL...YRL..F.FHWG......GSEH..D...YAAELHLVHWNTKY..F..A....DGLA.
Retrocopy SDKSVLSGGPLTERYRLAHFSFHWGCRDD-QGSEHSIDDLKYAAELHLVHWNTKYKTFCDALHHSDGLAI

Parental  IGVFLQVGHDKPELQKIINAMSNIRTKGENIAFTNFNPACLLPECLDYYTYPGSLTTPPLLECVTWIVLK
          .GVFL..G...PELQ..I.A...I........FT.FNPACLLP..LD..TY.GSLT.PPLLECV.WIVL.
Retrocopy VGVFLTIGNSEPELQEVIDALDAIKQRNMHAVFTDFNPACLLPDNLDFWTYSGSLTIPPLLECVVWIVLR

Parental  EPICLSHAQMKEFYCLYFTGVGEKPEKHMMCNWRPVQPLYDRTIKRSFK
          EPI.....Q...F..LY.T..GE.P..HM..NWRP.QPL..R...R..K
Retrocopy EPINITKEQLSKFRSLYSTTKGEYPQRHMVENWRPCQPLQGRQVRRFLK

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_121 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005408	1 retrocopy	retro_dnov_51,
Sarcophilus harrisii	ENSSHAG00000008895	1 retrocopy	retro_shar_121 ,