RetrogeneDB ID: retro_shar_98

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841307.1:43835..45293(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000002859
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000001207
• Aliases: None
• Description: None

Sequence

>retro_shar_98
ATGGCCGCGATCTGGCAGCAGGTGCTGGCCGTGGATGCAAGGTACAACGCATACCGCACGCCCACCTTCCCCCAGTTCCG
AACACAATACATACGGCGCCGGAGTCAGCTGCTGAGAGAAAATGCCAAGGCAGGGCACGAACCGGCCTTTCGAAGGCAGT
ACCTAAAGCTGAGGGCCCAGCTGCTGGGGCACCGCTACGGGCCTCTGACAGAGCCCGGGAGCTTCCGAGCCTTCAGCAAC
AGTGTTGTCCGAAGCAGTCGGACCACCCTGGACCGAATGGAGGACTTCGACGAGGACCCTCGTTCACTTGGTGCCCGTGG
CCACCGGCGCTCCGTTAGTCGCGGATCCTATCAGTTGCAGGCCCAGATGAATCGGGTCATCTACGATGAGAGGACGCTCG
GCAGTGTCGTGCCCACGTCGGTAGCCGAGGCCAGCCGGGCCATGGCGGGGGACACTTCGCTGAGTGAAAACTATGCTTTT
GCTGGGATGTACCACGTCTTTGACCAACATGTGGATGAGGCTGTTCCCAAAGTCCAATTTGCCAATGATGATCGCCACCT
GCTAGCCTGTTGCTCCCTGGATGGCAGCATCTCCGTGTGCCAGCTGGTACCCGCCCCCCCTGTGGTACTGCGTGTGCTCC
GTGGGCATTCGCGTGGCGTGTCCGACTTTGCCTGGTCCCTTTCCAATGACGTCCTCGTCTCCACGTCGCTGGATGCCACC
ATGCGCATCTGGGCCACGGAAGATGGCCGCTGCATCCGAGAGATCCCTGACCCGGATGGGGCAGAACTGCTGTGCTGCAC
TTTCCAGCCGATCAACAACAATCTCACTGTGGTGGGCAACGGGAAGCACAACGTGCACGTGATGAACATCTCCACGGGCA
AGAAAGTGAAGGGCGGCTCCAGCAAGCTGACTGGCCGCGTGCTGGCTCTGTCCTTTGATTCCCCCGGACACATCTTATGG
GCTGGGGACGATCGCGGCAGAGTCTTTTCCTTCCTTTTTGACGTGGCTACAGGGAAGCTGACCAAGGCCAAGCGGTTGCT
GGTACACGAAGGCAGCTCCATCACTAGCATCAGTGCGCGTTCCTGGATCAGCCGGGAAGCGCGAGACCCGTCTCTGCTCA
TTAACGCCTGCATCAACAAACTGCTTCTCTACCGGGTAGTGGATAACCAGGGCACTCTGCAGCTGAAGAGGAGCTTCCCC
ATTGATCAGAGCCAGCATCCCATTCGAAGTATCTTCTGCCCTCTCATGTCCTTCCGCCAGGGAGCCTGTGTGGTCACAGG
CAGCGAGGACATGTGTGTCTATTTCTTTGATGTGGAACGGACCTCCAAAGCCATCGTCAATAAACTGCAGGGCCATAGCG
CCGCCGTGTTGGATGTCAGTTTCAACTGTGACGAGAGCCTTCTGGCCTCGAGCGATGCAGTTGGGATGGTCATCGTGTGG
CGACGCGAACAAGAATAA

Alignment

ORF - retro_shar_98 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.82 %
• Parental protein coverage: 96.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYNAYRTPTFPQFRTQYIRRRSQLLRENAKAGHEPAFRRQYLKLRAQLLGHRYGPLSEPGSFRAYSNSVV
          .YNAYRTPTFPQFRTQYIRRRSQLLRENAKAGHEPAFRRQYLKLRAQLLGHRYGPL.EPGSFRA.SNSVV
Retrocopy RYNAYRTPTFPQFRTQYIRRRSQLLRENAKAGHEPAFRRQYLKLRAQLLGHRYGPLTEPGSFRAFSNSVV

Parental  RSSRTTLDRMEDFDEDPRSLGARGHRRSVSRGSYQLQAQMNRVIYDERMPGSVVPTSVAEASRAMAGDTS
          RSSRTTLDRMEDFDEDPRSLGARGHRRSVSRGSYQLQAQMNRVIYDER..GSVVPTSVAEASRAMAGDTS
Retrocopy RSSRTTLDRMEDFDEDPRSLGARGHRRSVSRGSYQLQAQMNRVIYDERTLGSVVPTSVAEASRAMAGDTS

Parental  LSENYAFAGMYHVFDQHVDEAVPKVQFANDDRHLLACCSLDGSISVCQLVPAPPVVLRVLRGHSRGVSDF
          LSENYAFAGMYHVFDQHVDEAVPKVQFANDDRHLLACCSLDGSISVCQLVPAPPVVLRVLRGHSRGVSDF
Retrocopy LSENYAFAGMYHVFDQHVDEAVPKVQFANDDRHLLACCSLDGSISVCQLVPAPPVVLRVLRGHSRGVSDF

Parental  AWSLSNDVLVSTSLDATMRIWATEDGRCIREIPDPDGAELLCCTFQPVNNNLTVVGNGKHNVHVMNISTG
          AWSLSNDVLVSTSLDATMRIWATEDGRCIREIPDPDGAELLCCTFQP.NNNLTVVGNGKHNVHVMNISTG
Retrocopy AWSLSNDVLVSTSLDATMRIWATEDGRCIREIPDPDGAELLCCTFQPINNNLTVVGNGKHNVHVMNISTG

Parental  KKVKGGSSKLTGRVLALSFDSPGHILWAGDDRGSVFSFLFDMATGKLTKAKRLVVHEGSSITSISARSWI
          KKVKGGSSKLTGRVLALSFDSPGHILWAGDDRG.VFSFLFD.ATGKLTKAKRL.VHEGSSITSISARSWI
Retrocopy KKVKGGSSKLTGRVLALSFDSPGHILWAGDDRGRVFSFLFDVATGKLTKAKRLLVHEGSSITSISARSWI

Parental  SREARDPSLLINACINKLLLYRVVDNEGTLQLKRSFPIDQSLHPIRSIFCPLMSFRQGACVVTGSEDMCV
          SREARDPSLLINACINKLLLYRVVDN.GTLQLKRSFPIDQS.HPIRSIFCPLMSFRQGACVVTGSEDMCV
Retrocopy SREARDPSLLINACINKLLLYRVVDNQGTLQLKRSFPIDQSQHPIRSIFCPLMSFRQGACVVTGSEDMCV

Parental  YFFDVERATKAIVNKLQGHSAAVLDVSFNCDESLLASSDAGGMVIVWRREQK
          YFFDVER..KAIVNKLQGHSAAVLDVSFNCDESLLASSDA.GMVIVWRREQ.
Retrocopy YFFDVERTSKAIVNKLQGHSAAVLDVSFNCDESLLASSDAVGMVIVWRREQE

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_98 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	ENSSHAG00000001207	1 retrocopy	retro_shar_98 ,