RetrogeneDB ID: retro_shar_111

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841485.1:1411646..1413200(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000014168
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ALDH1A2
• Ensembl ID: ENSSHAG00000012217
• Aliases: None
• Description: aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:15472]

Sequence

>retro_shar_111
ATGCTGCGTCTCCTGGCCCCCCGGTTATCTGGTCTTTGTAGAAAGGTTGCTCCCTTCTCATCTGCTGCGAATCTTCCGAA
CCCTGTGCTACAGCCAGATGTTCGCTATGACAAACTCTTCATCAATAACGAGTGGAGGGATGCAGTCAGCAAGAAGACAT
TCCCAACGGTCAATCCCTCCACGGGAGAGGTCATCACTCATGTGGCTGAAGGGGATAAGGCAGATGTGGACTTGGCTGTC
AAAGCTGCCCGGGAAGCCTTTCGGCTGGGGTCACCATGGCGACAGATGGATGCTTCTGAAAGGGGGCGTCTGCTTTACCG
CCTAGCTGACCTGGTAGAGAGAGATCGTGTCTACCTAGCCTCCCTGGAGACTCTGGACAATGGCAAGCCTTTCCAAGAGT
CCTATGTCCTAGACCTTGATGAGGTCATTAAGGTGTATCGGTACTTTGCAGGCTGGGCAGACAAATGCCACGGGAAGACC
ATCCCTATGGATGGAGAGCATTTCTGCTTCACAAGGCATGAGCCTGTTGGAGTGTGTGGCCAGATCATTCCATGGAACTT
CCCTTTGGTCATGCAAGGCTGGAAACTTGCCCCAGCTCTTGCTGCCGGCAATACTGTTGTCATGAAGGTGGCTGAACAGA
CCCCACTCTCTGCCTTGTACTTTGCCTCCTTGATTAAAGAAGCTGGCTTTCCTCCCGGAGTTGTAAACATCATCACAGGC
TATGGACCTACTGCAGGGGCTGCTGTGGCCCAACACATGGACATTGATAAAGTGGCCTTTACTGGCTCTACCGAGGTTGG
GCATCTGATCCAGAAGGCAGCAGGAGACTCCAACCTGAAGAGGGTCACGCTAGAGCTGGGGGGGAAGAGCCCCAGTATTG
TCCTGGCAGACGCAGACATGAATCACGCTGTGGAGCAGTGTCATGAAGCCCTCTTCTTCAACATGGGTCAGTGCTGTTGT
GCAGGTTCTCGGACCTTTGTGGAAGACTCTATCTATGATGAATTTCTTGAAAGGACTGTGGAAAAAGCCAAACAGAGGAA
AGTTGGGAATCCCTTTGAGCTTGACACACAGCAAGGGCCCCAGGTGGACAAGGAGCAATTTGAAAAAATCCTGAGTTACA
TCCAAGTGGGCCAGAAAGAAGGCGCTAAGTTGATGTGTGGGGGAGAACGCTTTGGGGAGAAGGGCTTCTTCATCAAGCCC
ACTGTCTTTGGCAATGTACAAGACAGCATGAGGATTGCCAAGGAAGAGATCTTTGGGCCCGTGCAGCCCGTCTTCAAGTT
CAAAAAGATCAGTGAGGTTATTGAGAGAGCCAACAATACCAAGTATGGATTGGCGGCGGCAGTGTTTACCAAGGACCTGG
ACAAGGCTATGTATTTGACCCAAGCCCTGCAAGCTGGAACTGTGTGGGTCAATACCTATAACATTGTAACATGTCATACT
CCTTTTGGAGGCTTCAAGGAATCTGGAAATGGAAGAGAGCTAGGGGAAGATGGGCTCAGAGAATATGTGGAAGTAAAGAC
TGTAACAGTGAAAATTCCTCAGAAAAATTCATGA

Alignment

ORF - retro_shar_111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.55 %
• Parental protein coverage: 95.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPSPTLNLEIKYTKIFINNEWQNSESGRVFPVYNPATGEQLCEVQEADKADIDKAVRAARLAFSLGSVWR
          LP.P.L.....Y.K.FINNEW....S...FP..NP.TGE....V.E.DKAD.D.AV.AAR.AF.LGS.WR
Retrocopy LPNPVLQPDVRYDKLFINNEWRDAVSKKTFPTVNPSTGEVITHVAEGDKADVDLAVKAAREAFRLGSPWR

Parental  RMDASERGRLLDKLADLVERDRAVLSTMESLNGGKPFLQAFYVDLQGVIKTLRYYAGWADKIHGMTIPVD
          .MDASERGRLL..LADLVERDR..L...E.L..GKPF......DL..VIK..RY.AGWADK.HG.TIP.D
Retrocopy QMDASERGRLLYRLADLVERDRVYLASLETLDNGKPFQESYVLDLDEVIKVYRYFAGWADKCHGKTIPMD

Parental  GDYFTFTRHEPIGVCGQIIPWNFPLLMFAWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGV
          G..F.FTRHEP.GVCGQIIPWNFPL.M..WK.APAL..GNTVV.K.AEQTPLSALY...LIKEAGFPPGV
Retrocopy GEHFCFTRHEPVGVCGQIIPWNFPLVMQGWKLAPALAAGNTVVMKVAEQTPLSALYFASLIKEAGFPPGV

Parental  INILPGYGPTAGAAIASHVGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAV
          .NI..GYGPTAGAA.A.H..IDK.AFTGSTEVG.LIQ.AAG.SNLKRVTLELGGKSP.I..ADAD...AV
Retrocopy VNIITGYGPTAGAAVAQHMDIDKVAFTGSTEVGHLIQKAAGDSNLKRVTLELGGKSPSIVLADADMNHAV

Parental  EQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVRRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELI
          EQ.H...FFN.GQCC.AGSR.FVE.SIY.EF..R.VE.AK.R.VG.PF...T.QGPQ.DK.Q..KIL..I
Retrocopy EQCHEALFFNMGQCCCAGSRTFVEDSIYDEFLERTVEKAKQRKVGNPFELDTQQGPQVDKEQFEKILSYI

Parental  QSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTVDEVIERANNSDLGL
          Q.G..EGAKL.CGG...G.KGFFI.PTVF.NV.D.MRIAKEEIFGPVQ....FK...EVIERANN...GL
Retrocopy QVGQKEGAKLMCGGERFGEKGFFIKPTVFGNVQDSMRIAKEEIFGPVQPVFKFKKISEVIERANNTKYGL

Parental  VAAVFTNDINKALTVSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGECGLREYSEIKTVTIKIPQ
          .AAVFT.D..KA.....A.QAGTVW.N.YN......PFGGFK.SGNGRE.GE.GLREY.E.KTVT.KIPQ
Retrocopy AAAVFTKDLDKAMYLTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGRELGEDGLREYVEVKTVTVKIPQ

Parental  KNS
          KNS
Retrocopy KNS

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_111 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006418	1 retrocopy	retro_chof_1106,
Dasypus novemcinctus	ENSDNOG00000010541	1 retrocopy	retro_dnov_2235,
Erinaceus europaeus	ENSEEUG00000012262	1 retrocopy	retro_eeur_15,
Monodelphis domestica	ENSMODG00000008641	1 retrocopy	retro_mdom_254,
Pan troglodytes	ENSPTRG00000007113	1 retrocopy	retro_ptro_118,
Sorex araneus	ENSSARG00000012720	1 retrocopy	retro_sara_40,
Sarcophilus harrisii	ENSSHAG00000012217	1 retrocopy	retro_shar_111 ,
Sarcophilus harrisii	ENSSHAG00000013162	1 retrocopy	retro_shar_758,
Tarsius syrichta	ENSTSYG00000004549	1 retrocopy	retro_tsyr_8,
Tursiops truncatus	ENSTTRG00000002361	1 retrocopy	retro_ttru_932,