RetrogeneDB ID: retro_shar_83

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867587.1:1761..2943(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000000566
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000010060
• Aliases: None
• Description: None

Sequence

>retro_shar_83
ATGTCCGCGCACGCCCAGATGCGTGCTATGCTGGACCAGCTGATGGGCACCTCCCGGGACGGAGACACTACCCGCCAGCG
AATCAAATTCAGCGATGACAGAGTCTGCAAGAGCCACCTTCTCAACTGCTGTCCTCATGATGTTCTTTCTGGAACCAGGA
TGGACCTGGGAGAGTGTCTGAAGGTCCATGATCTGGCTTTGAGAGCAGATTATGAAATCGCCTCCAAAGAACAGGACTTT
TTCTTTGAGCTCGATGCCATGGACCATCTGCAGTCATTCATTGCAGACTGTGATAGGAGAACCGAAGTGGCCAAGAAAAG
GCTAGCAGAGACTCAGGAAGAGATTAGCGCCGAAGTGGCAGCCAAAGCCGAACGTGTCCATGAACTTAATGAGGAAATTG
GCAAGTTACTGGCCAAAGTAGAGCAGCTGGGAGCTGAAGGGAACGTGGAAGAGTCCCAGAAAGTGATGGACGAAGTAGAA
AAAGCCCGAGCAAAGAAAAGAGAGGCGGAAGAGGTCTACCGGAATTCCATGCCGGCTTCCAGCTTCCAACAACAGAAACT
TCGAGTTTGTGAAGTATGTTCTGCTTATTTGGGTCTTCATGACAATGACAGGCGACTAGCCGACCATTTTGGGGGGAAAC
TGCACCTGGGATTTATTGAGATAAGAGAGAAGCTTCAAGAGCTCAAGAGAGTTGTGGCTGAGAAGCAAGAGAAAAGAAAT
CAGGAACGCCTGAAACGCAGAGAAGAGAGAGAGAGAGAAGAAAGGGAGAAGTTGAGAAGATCCAGATCACACAGCAAGAA
TCCCAAAAGATCTCGATCCCGGGAGCATAGGAGACATCAGTCTCGGTCCACTTCCCAAGAAAGGAAGAGAACCAGATCCA
AGTCTCACGAGAAACGGCATCGTCACAGGTCGCGCTCCAGCAGCCGCAGCCACCAGAGAAGCAGGCATAGCTCCAGAGAC
CGGAGCAGAGAGCAGCCCAAGAGAAGATCCTCAAAAGAAAGGTATTCTGGAGATAAAGAGAGGTCCTTACGAGACCAAGA
TCTAACATCACGTGACAAAGACAGGAGCTCCAGGTCACCACGGGACAGAGAGACAAAACACAAGAAACGTTCCTATGAGA
GTGCTAATGGCCGTTCAGAAGACAGAAGGAGCTCTGAAGAGCCTGAAGCTGGGGAGATTTAA

Alignment

ORF - retro_shar_83 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.26 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDTTRQRIKFSDDRVCKSHLLNCCPHDVLSGTRMDLGECLKVHDLALRADYEIASKEQDFFFELDAMDHL
          GDTTRQRIKFSDDRVCKSHLLNCCPHDVLSGTRMDLGECLKVHDLALRADYEIASKEQDFFFELDAMDHL
Retrocopy GDTTRQRIKFSDDRVCKSHLLNCCPHDVLSGTRMDLGECLKVHDLALRADYEIASKEQDFFFELDAMDHL

Parental  QSFIADCDRRTEVAKKRLAETQEEISAEVAAKAERVHELNEEIGKLLAKVEQLGAEGNVEESQKVMDEVE
          QSFIADCDRRTEVAKKRLAETQEEISAEVAAKAERVHELNEEIGKLLAKVEQLGAEGNVEESQKVMDEVE
Retrocopy QSFIADCDRRTEVAKKRLAETQEEISAEVAAKAERVHELNEEIGKLLAKVEQLGAEGNVEESQKVMDEVE

Parental  KARAKKREAEEVYRNSMPASSFQQQKLRVCEVCSAYLGLHDNDRRLADHFGGKLHLGFIEIREKLEELKR
          KARAKKREAEEVYRNSMPASSFQQQKLRVCEVCSAYLGLHDNDRRLADHFGGKLHLGFIEIREKL.ELKR
Retrocopy KARAKKREAEEVYRNSMPASSFQQQKLRVCEVCSAYLGLHDNDRRLADHFGGKLHLGFIEIREKLQELKR

Parental  VVAEKQEKRNQERLKRREEREREEREKLRRSRSHSKNPKRSRSREHRRHRSRSTSRERKRRTRSKSREKR
          VVAEKQEKRNQERLKRREEREREEREKLRRSRSHSKNPKRSRSREHRRH.SRSTS.ERK.RTRSKS.EKR
Retrocopy VVAEKQEKRNQERLKRREEREREEREKLRRSRSHSKNPKRSRSREHRRHQSRSTSQERK-RTRSKSHEKR

Parental  HRHRSRSSSRSRSRSHQRSRHSSRDRSRERSKRRSSKERSSGDKERSLRDQDLASRDKDRSSRERSPRDR
          HRHRSRSSSRS....HQRSRHSSRDRSRE..KRRSSKER.SGDKERSLRDQDL.SRDKDRSS..RSPRDR
Retrocopy HRHRSRSSSRS----HQRSRHSSRDRSREQPKRRSSKERYSGDKERSLRDQDLTSRDKDRSS--RSPRDR

Parental  ERKDKKRSYESANGRSEDRRSSEEREAGEI
          E.K.KKRSYESANGRSEDRRSSEE.EAGEI
Retrocopy ETKHKKRSYESANGRSEDRRSSEEPEAGEI

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_83 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013748	1 retrocopy	retro_mdom_2011,
Mus musculus	ENSMUSG00000029823	1 retrocopy	retro_mmus_2440,
Sarcophilus harrisii	ENSSHAG00000010060	1 retrocopy	retro_shar_83 ,