RetrogeneDB ID: retro_shar_169

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834520.1:90045..90598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000016712
• Aliases: None
• Description: None

Sequence

>retro_shar_169
TATGTAGACACTTTAGAGGAGATTAATTACCCTGTAGCAGCATATGAGCAAATTGCTTCTGCTGCTATCAAAGCATGGGG
CACCCTTGCAGGGAGACAAAATAGAGGAGAAGCCTTCTCGAAAATAGCAGAAGGACCAAATGAACCTTTGCTGATTTTGT
GGGACATCTGCAGACAGCTGTCATACGAACTATTGAAATGCAGCAACAGAAATTATGATAAGACAACTTGGTAGAGAAAA
TGCTAATGAAATTTGTAGAAGAATTATACTAGGACTACACAAGGATGCTCCTTTAGATGAGATCATAAGGCATTGTGCCA
CAGTGGGCACAAATACCTTTTATACCCAGGCTATGATGAACATGGGAAGATAGGGTCCCTTTTGGCAAGGGACTTCCAAA
GAGATTCATCAATGCTTCCAATGTGGTAAAGTAGGACATCTGAAAGCTCCATGTTGGCATAAAACACAGGGTGGGAAAAA
AAAGACCCAAAACCCCATGTCCAAAATGCAACAGAGGCTTCCATTGGGCATCAGAATGTAGACTGACTCAGTA

Alignment

ORF - retro_shar_169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 60.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YVDTSAQINNPIAAYEQIASAAIKAWGFSPGKQGRREAFTKIAQGPNE-SFADFVGRLQTAVIM-NYDEN
          YVDT...IN.P.AAYEQIASAAIKAWG...G.Q.R.EAF.KIA.GPNE..FADFVG.LQTAVI..NY..N
Retrocopy YVDTLEEINYPVAAYEQIASAAIKAWGTLAGRQNRGEAFSKIAEGPNE<TFADFVGHLQTAVIR<NY*-N

Parental  AATEIMIRQLVK-NANEVCRRIILGLYKDAPLEKIIRHCATVGTNTFYSQVFPRSKHGKTGSLLARATCQ
          AATEIMIRQL...NANE.CRRIILGL.KDAPL..IIRHCATVGTNTFY.Q.......G..G.........
Retrocopy AATEIMIRQLGRENANEICRRIILGLHKDAPLDEIIRHCATVGTNTFYTQAM--MNMGR*GPFWQGTSKE

Parental  FFQC---GKVGHLKAQCWHKIDSG-KQDGGPSSRAQSNLVMVVQILTLTV
          ..QC...GKVGHLKA.CWHK...G......P.S..Q..L.......T..V
Retrocopy IHQCFQCGKVGHLKAPCWHKTQGGXXXTQNPMSKMQQRLPLGIRM*TDSV

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_169 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000009835	3 retrocopies	retro_shar_151, retro_shar_195, retro_shar_429,
Sarcophilus harrisii	ENSSHAG00000016712	2 retrocopies	retro_shar_169 , retro_shar_562,