RetrogeneDB ID: retro_shar_92

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867787.1:653..2000(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000000367
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000012259
• Aliases: None
• Description: None

Sequence

>retro_shar_92
ATGTCTGAAGTGGCTAGGCAGCTGAAGGAGCTCGTATGGGGGTCAAACACTAACCCTGGTCTCTCAGACCCCATATTTGA
TCGCTGGACACAGGGCTTCGTATTCAGTGAGGCAGAAGGCTCAGCCCTGGAGCAGTTTGAGGGGGGCCCATGTGCTGTCA
TCGCTCCTGTTCAGGCATTCCTTTTGAAGAAACTGTTGTTCGCCTCAGAGAAGACTTCCTGGAGAGACTGTCGAGAGGAT
GAGCGGAAGGATTTGCTGTGCCATACCTTGTGTGACATCTTACAAGCAGCTTGCTTTAACAGCTCGGGTCCCTACTGCTT
GGCTGCGTGCAAGGTTAGAGGAAAGGAGACCGTTGGCTTGTCAGATAGGCCAACTGCTGGGGGTGAGTGTAGTTGTCAGA
GGGGTCACTCCTCGTTAGCCGTGGCCACCCAAGATCATCTGAGCTTTGAGCGATTCCACTCATTAATTCGGAGGATTTCA
TTCAAAAGTTTCCCTGAGCTCAAAGATGCCATCTGTGATCAGTATTCTATATGGGCCAATAAATTTGGGGTGTTACTTTT
TCTTTATTCCGTGATACTAACCAAAGGTATTGAAAACATAAAAAAAGAAATTGAGGATTCAGCAGAACCATTGATTGATC
CCGTCTATGGTTATGGTAGCCAAAGTCTAATTAACCTGCTCTTAACTGGGCATGCAGTTTCTAATGTATGGGATGGAGAT
AAAGAGTGCTCTGGAATGAAGCTTCTAGGCATACATAAGCAGTCTACAGTGGGCTTCTTAACACTTATGGAGTCACTGAG
TTATTGCAAGGTCGGCTCCTATTTGAAATCACCTAAGTTTCCTATTTGGATTGTTGGTAGCGAAACTCACCTTACTGTTT
TATTTGCTAAGGATATGGCCCTGGTGCCTCCTGAGACACCTTATGAGCAAGCCAGGAGGATTTTTCAGACATATGATCCT
GAAGATAATGGATTTATACCAGATACGCTATTAAAGCATGTGATGAAAGCATTGAATCTGGTTTCAGATGCTGAATGTGT
TAGAGTTATGAAAAACAAATTAGACCCCGAAGGCCTAGGAATTATATTACTAGGTCCTTTCCTCCAAGAATTTTTCCCAG
AGCAGAATTCAAACGTGCCTGAGTCCTTTACTGTATACCACTATAATGGACTAAAACAGTCCAATTTTAATGAAAAGGTC
ATGTATGTAGAAGGCACAGCAGTTGTAATGGGTTTTGGAGAGTGTTTGCTGCATACAGATGACACACCAGTTAAACGCTG
TCTGCAAACAAAATGGCCATCCATAGAATTGCTTTGGACAACTGATAGATCTCCTTCATTAAACTAA

Alignment

ORF - retro_shar_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSELTKELMELVWGPKSSPGLSDTIFCRWTQGFVFSESEGSALEQLEGGPCAVIAPVQAFLLKKLLFTSE
          MSE....L.ELVWG....PGLSD.IF.RWTQGFVFSE.EGSALEQ.EGGPCAVIAPVQAFLLKKLLF.SE
Retrocopy MSEVARQLKELVWGSNTNPGLSDPIFDRWTQGFVFSEAEGSALEQFEGGPCAVIAPVQAFLLKKLLFASE

Parental  KSSWRDCQEEERKDLLCHTLCDILETACSENSGSYSLAAW-IRGKTTEDTASISEGPAESSCQEEHTS-A
          K.SWRDC.E.ERKDLLCHTLCDIL..AC...SG.Y.LAA...RGK.T...........E.SCQ..H.S.A
Retrocopy KTSWRDCREDERKDLLCHTLCDILQAACFNSSGPYCLAACKVRGKETVGLSDRPTAGGECSCQRGHSSLA

Parental  LAVEE-LGFERFHSLIHKKSFKSFPELKEAIWDQYSMWANKFGVLLFLYSVILTKGIENIKNEIEDSTEP
          .A....L.FERFHSLI...SFKSFPELK.AI.DQYS.WANKFGVLLFLYSVILTKGIENIK.EIEDS.EP
Retrocopy VATQDHLSFERFHSLIRRISFKSFPELKDAICDQYSIWANKFGVLLFLYSVILTKGIENIKKEIEDSAEP

Parental  LIDPVYGHGSQSLINLLLTGHAVSNVWDGDRECSGMKLLGIHKQATIGFLTLMESLRYCKVGSYLKSPKF
          LIDPVYG.GSQSLINLLLTGHAVSNVWDGD.ECSGMKLLGIHKQ.T.GFLTLMESL.YCKVGSYLKSPKF
Retrocopy LIDPVYGYGSQSLINLLLTGHAVSNVWDGDKECSGMKLLGIHKQSTVGFLTLMESLSYCKVGSYLKSPKF

Parental  PIWIVGSETHLTVFFAKDMALVAPEAPSEQARRVFQTYDPEDNGFIPDTLLEDVMKALDLVSDPEYVNLM
          PIWIVGSETHLTV.FAKDMALV.PE.P.EQARR.FQTYDPEDNGFIPDTLL..VMKAL.LVSD.E.V..M
Retrocopy PIWIVGSETHLTVLFAKDMALVPPETPYEQARRIFQTYDPEDNGFIPDTLLKHVMKALNLVSDAECVRVM

Parental  KNKLDPEGLGIILLGPFLQEFFPDQDSSVPESFTVYHYNGLKQSNYNEKVMYVEGTAVVMGFEDPMLQTD
          KNKLDPEGLGIILLGPFLQEFFP.Q.S.VPESFTVYHYNGLKQSN.NEKVMYVEGTAVVMGF....L.TD
Retrocopy KNKLDPEGLGIILLGPFLQEFFPEQNSNVPESFTVYHYNGLKQSNFNEKVMYVEGTAVVMGFGECLLHTD

Parental  DTPVKRCLQTKWPYIELLWTTDRSPSLN
          DTPVKRCLQTKWP.IELLWTTDRSPSLN
Retrocopy DTPVKRCLQTKWPSIELLWTTDRSPSLN

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_92 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
Monodelphis domestica	ENSMODG00000010034	1 retrocopy	retro_mdom_183,
Sarcophilus harrisii	ENSSHAG00000012259	1 retrocopy	retro_shar_92 ,