RetrogeneDB ID: retro_shar_644

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856909.1:397145..398425(+)
• Located in intron of: ENSSHAG00000007960

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHUK
• Ensembl ID: ENSSHAG00000000038
• Aliases: None
• Description: conserved helix-loop-helix ubiquitous kinase [Source:HGNC Symbol;Acc:1974]

Sequence

>retro_shar_644
CTGCAATATCTGGCCCCAAAGCTCTTTGAGAACAAGCTATTTACTGCTACTACTGATTGGAGCTTTGAGACAACAATGTT
TGAATACAGAGTGAAATAAAGACCTGTCCTACATCATACTTGGCATAAGATTAAAAACAATGATCCCAAGCACATATTTC
TATTTAAAGAGATGACTGGAGAAGCTGGATTTAGTAGCCATTTTTCTCAATTAAGTAAGTCTCTCTAGTTTCATAGTAGA
GCCCATGGAGTAATAGTTTCAGTTGATGATGCCTTTGAGATCCTTAGCAGAGAGGATGAAGTCTGGATCTCATGCTTAAA
CAGCCAAGATGCTTTGTGTTGATGGACCACATACTGAACTTGAAGATAGTACATATGTCAAATATGAATGTTACAAGGAT
AATTTCCTTCCTGTTACTGCCTGAGGAGAATCTTCATTCACTAAAATCTCGATTTGAGCATGAACGTGGAATAAATACAG
CTTCTCAAAACTGTTCTTAGAGATGAGAATTTCTCTGTACCCTCCTCCCTGGTAGCTTGTCTCTCAGTGTGTTTAAATAG
AGTATGAAGCTGTGATAGTTACATGGAATATTGTTTGATAAAAGTGAGATCATCTATGAAAACCCCTTTGCTTTCAGAAG
TTTATTTGAATGTGTAAATAATACTGTAAAAGGACAGCAAAATCCAATTCACAGTCATGCAGCTGCATAGAATGTGGACT
GAAGCTATGAATTATGTGTCTGGATTCAAGGATGGATACAGCAGGCTCTTTCAGGGGCAGAGAGCAGCAATATTGAGTCT
TCTTTGCTGTAATGCTAACTTAACAAAAATTAAGAACACCATAATCTCAGCATCTCAAAAACTGAAAGCAAAATTACAGT
TTTTTCATCAGAGCATTCAGTTTGACCTGACTAGATAACAGTGATTACATGACTAATGCGATATCCTCAGGAAAAAAATG
CCTGGAAAGCAATGGAAGAAAAAGCCATCTAGAATGTACAAGCTGGTGATATTGAATACTTGGGTGAGCAAATCATATCC
CTGCAAACAAAAATTGTGGAGCTGCAGAGGAGCCCTTCTATAAGGTATCAGGAAGATGTACTGGAATCTCTGAAAATGAA
AGCCATTGATCCCTCCAGGCATTTGAAGCCCAAGTCTTCAGATCACTTCTACATTGACAGCTCCCAGATGATAAAGATCA
ATGTGCTGACCACAGAGAACCAGAACTGCATAGTCAAGGAGTCTTTTGGTCACCTTGGCAAGTAATTGGGCTGTAAGCAA

Alignment

ORF - retro_shar_644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.87 %
• Parental protein coverage: 58.54 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  LQYLAPELFENKPYTATVDYWSFGTMVFECIVGYRPFLHHLQPFTWHEKIKKKDPKHIFAFEEMTGEVRF
          LQYLAP.LFENK..TAT.D.WSF.T..FE..V..RP.LHH....TWH.KIK..DPKHIF.F.EMTGE..F
Retrocopy LQYLAPKLFENKLFTATTD-WSFETTMFEYRVK*RPVLHH----TWH-KIKNNDPKHIFLFKEMTGEAGF

Parental  SSHLPQPN-SLSSFIVEPMEQWLQLMLTW-DPQQRGGSLDLTLKQPGCFVLMDQILNLKIAHILNMTSAK
          SSH..Q...SLSSFIVEPME...QLM....DP.QRG.SLDL.LKQP.CFVLMD.ILNLKI.H..NM....
Retrocopy SSHFSQLS>SLSSFIVEPME**FQLMMPL>DP*QRG*SLDLMLKQPRCFVLMDHILNLKIVHMSNMNVTR

Parental  IISFLLLPEESFHSLQSRIEQETGISTASQ-ELLLEMGISL--DPRKPASQCV-LDGVRGCDSYMVY-LF
          IISFLLLPEE..HSL.SR.E.E.GI.TASQ..L.LEM.ISL...P....SQCV.L..V..CDSYM.Y.LF
Retrocopy IISFLLLPEENLHSLKSRFEHERGINTASQ<KLFLEMRISLYPPPW*LVSQCV<LNRV*SCDSYMEY<LF

Parental  DKSKIVYEGPFASRSLSECVNYIVK-DSKIQLPVMQLRRVWAEAVHYVSGLKEDYSRLFQGQRAAMLSLL
          DKS.I.YE.PFA.RSL.ECVN..VK.DSKIQ..VMQL.R.W.EA..YVSG.K..YSRLFQGQRAA.LSLL
Retrocopy DKSEIIYENPFAFRSLFECVNNTVK>DSKIQFTVMQLHRMWTEAMNYVSGFKDGYSRLFQGQRAAILSLL

Parental  RYNANLTKMKNTMISASQQLKAKLQFFHQSIQLDLDR-YSDQMTYGISS-EKMLKAWKEMEEKAIQCAQA
          ..NANLTK.KNT.ISASQ.LKAKLQFFHQSIQ.DL.R..SD.MT..ISS.EK...AWK.MEEKAI...QA
Retrocopy CCNANLTKIKNTIISASQKLKAKLQFFHQSIQFDLTR>NSDYMTNAISS>EK--NAWKAMEEKAI*NVQA

Parental  GDIGYLDEQIMSLHTEIVELQRSPSARRQEDVMESLEQKAIDLYKQLKPRSPDHSYSDSSEMVKIIVLTV
          GDI.YL.EQI.SL.T.IVELQRSPS.R.QEDV.ESL..KAID....LKP.S.DH.Y.DSS.M.KI.VLT.
Retrocopy GDIEYLGEQIISLQTKIVELQRSPSIRYQEDVLESLKMKAIDPSRHLKPKSSDHFYIDSSQMIKINVLTT

Parental  QNQDRVLKELFGHLSKLLGCKQ
          .NQ....KE.FGHL.K.LGCKQ
Retrocopy ENQNCIVKESFGHLGK*LGCKQ

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_644 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
Mus musculus	ENSMUSG00000025199	1 retrocopy	retro_mmus_1521,
Sarcophilus harrisii	ENSSHAG00000000038	1 retrocopy	retro_shar_644 ,
Ictidomys tridecemlineatus	ENSSTOG00000016412	1 retrocopy	retro_itri_1711,