RetrogeneDB ID: retro_shar_89

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864885.1:415054..416200(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000008387
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000018681
• Aliases: None
• Description: None

Sequence

>retro_shar_89
ATGTCTGAGTTCTGGCTTATATCAGTTCCTGGGGATAAAACCTGCCAACAAGCATGGGAGAAACTACAGGCAGCAACAAC
CAAAACTAATCTCTCCACTAATTCAAAGTTCAGCATTCCTGAATTAAAGATCGGCACGCTGGATGTTTTAATCAGTTTAT
CAGACGAACTGGACAAACTGGATTCCTTTGCGGAAATAAATGTTAAGGAAATGTCTAAATATATGGCCGAAGTTCTAGAG
GATAGCGAAGATAAAGCTGGAGAAATCCTATTGGTGGATGGACTCGACTTAGTGACGTATCTAACAAGGTTCCAATGGAA
TATGGCCAAGTACCCAATCACGGAATCCCTGAAAAGTCTTGCCGAAATGATGGCCAAGGGAGCCAAACAAATTAGTAATG
ATTTCAGAGCCCGATCGTCTTCCTACAACGAACTGAAAGTAAATATTCAGAATTGGGAAAAAAAGAATGCAGGAAGTTTA
TTAACTAGAAGCCTAGTAGAAATTGTAAAGAAAGAGGACTTTGTCCTTGATTCAGAATATCTCATCACATTATTGGTAGT
AGTTCCCAAGTCACATCATAATGACTGGGTTAAGCAATATGAAACACTAGTCGACATGGTAGTCCCAAGGTCTAGCCAGG
TTATTTCAGAGGACCAAGATAATTACCTATGCAATGTTACTTTATTTAGAAAGGCAGTGACAGACTTCATAAAAAAAGCC
AGAGAGAAGAAATTCGTTGTTCGGGATTTTCAGTATGATGAAGAACAGATAAAAGCAGACAAAGAAGAGGTGGCAAATAT
CTCCACTGACAGGAAGAATAAACTTGGACTATTAATTAGGTGGCTGAGAGTGAATTTCAGTGAAGCTTTCGTAATATGGA
TTCATGTGAAAGCATTAAGAGTTTTTGTTGAGTCTATTTTAAGATATGGATTGCCAATGAACTTCCAGGCAATACTACTT
CAACCCAATAAGAAAAACATAAAGAAACTGAGAGAGGTACTGTATGATTTATACAAACATCTGGATGATAGTTCAGGAGC
TATTATTGATTTTGCTACGGATGTTCAAGCCTATAAGCTCAATGACCAGGAATATTATCCCTATGTATTCTTCAAGGTTG
ATTGCAATCCAATACAATTAAAGTAA

Alignment

ORF - retro_shar_89 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEFWLISAPGEKTCQQTWEKLHAATTKSNNLSINSKFNIPDLKVGTLDVLVGLSDELAKLDSFVEGVVK
          MSEFWLIS.PG.KTCQQ.WEKL.AATTK.N.LS.NSKF.IP.LK.GTLDVL..LSDEL.KLDSF.E..VK
Retrocopy MSEFWLISVPGDKTCQQAWEKLQAATTKTN-LSTNSKFSIPELKIGTLDVLISLSDELDKLDSFAEINVK

Parental  KVAQYMADVLEDSRDKVQENLLANGVDLITYITRFQWDMAKYPIKQSLKNISEIIAKGVNQIDNDLKARA
          ....YMA.VLEDS.DK..E.LL..G.DL.TY.TRFQW.MAKYPI..SLK...E..AKG..QI.ND..AR.
Retrocopy EMSKYMAEVLEDSEDKAGEILLVDGLDLVTYLTRFQWNMAKYPITESLKSLAEMMAKGAKQISNDFRARS

Parental  SAYNNLKGSLQNLERKNAGSLLTRSLAEIVKKDDFVLDSEYLITLLVVVPKLNHNDWVKQYETLAEMVVP
          S.YN.LK...QN.E.KNAGSLLTRSL.EIVKK.DFVLDSEYLITLLVVVPK..HNDWVKQYETL..MVVP
Retrocopy SSYNELKVNIQNWEKKNAGSLLTRSLVEIVKKEDFVLDSEYLITLLVVVPKSHHNDWVKQYETLVDMVVP

Parental  RSSKVLSEDQDSYLCNVTLFRKAVDDFRHKARENKFIVRDFQYNEEEMKADKEEMTRLSTDKKKQFGPLV
          RSS.V.SEDQD.YLCNVTLFRKAV.DF..KARE.KF.VRDFQY.EE..KADKEE....STD.K...G.L.
Retrocopy RSSQVISEDQDNYLCNVTLFRKAVTDFIKKAREKKFVVRDFQYDEEQIKADKEEVANISTDRKNKLGLLI

Parental  RWLKVNFSEAFIAWIHVKALRVFVESVLRYGLPVNFQAMLLQPNRKTMKKLREVLYDLYKHLDSSAAAII
          RWL.VNFSEAF..WIHVKALRVFVES.LRYGLP.NFQA.LLQPN.K..KKLREVLYDLYKHLD.S..AII
Retrocopy RWLRVNFSEAFVIWIHVKALRVFVESILRYGLPMNFQAILLQPNKKNIKKLREVLYDLYKHLDDSSGAII

Parental  DAPMDIPGLNLTQQEYYPYVYYKIDCNLLEFK
          D...D.....L..QEYYPYV..K.DCN....K
Retrocopy DFATDVQAYKLNDQEYYPYVFFKVDCNPIQLK

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_89 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000011909	1 retrocopy	retro_lafr_406,
Sarcophilus harrisii	ENSSHAG00000009886	1 retrocopy	retro_shar_33,
Sarcophilus harrisii	ENSSHAG00000018681	1 retrocopy	retro_shar_89 ,
Tarsius syrichta	ENSTSYG00000006233	1 retrocopy	retro_tsyr_1134,