RetrogeneDB ID: retro_shar_100

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834451.1:1463055..1465245(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000014363
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000014095
• Aliases: None
• Description: None

Sequence

>retro_shar_100
ATGAGTCTGGACAAGAAGAGAAGCGCCCCGTACCACCAGATGAAGAAGCCGCGGGACGAGCCCCCGCCCATAGCCCGCCC
TCTGAGGAGAGAGCTCCCGCGGGAAAAGGGAGCCGCGGGCAGGGGGCCTTCCAGGGTGACCAGCACCGTGAGGAAGCTCC
TGGGGCCCAACCCCCACCCCGGCATGAGGCAGGAGCTCATCAGGCTCGTTGCAGCAAAGAGAGAAAAGGAGTACGTCAAT
TTCCGGACGTTTAGATTGTTTGCTGGAACGTGGAACGTGAATGGCCAGCCCCCGGACTGCGGGCTGGAACTGTGGCTCAG
TTGTGACCGGGACCCGCCGGACATTTACTGCCTCGGGTTCCAGGAGCTGGATTTGAGCATGGAGGCCTTCTTCTACTTGG
AATCGGCCAGGGAGCACGAGTGGCTGGCGTCGGTGAAGCAAGCGTTGCACGCCAAGTCCAAGTACAAGAAGGTGCAGCTG
GTGCGCCTGGTGGGGATGCTGCTGCTGATCTTCGCCAGGAAGGAGCACTGCGGGCACATCCAGGACGTGGTGACGGACAC
CGTGGGCACGGGGCTCATGGGGAAGATGGGGAACAAGGGCGCCGTGGCGGTGAGGTTCATGTTCCACAACACCAGCTTCT
GCGTCGTCAATTCCCACCTGGCCGCCCAGGGCGAGGACGTTGAGGGCAGGAACCAGGACTACAAGGACATCTGTGCCCGG
ATGAATTTCTTCGTCCCGAATCAGGGCCAGCTGAACATCATGAAGCACGATGTTGTCATCTGGCTGGGGGACCTGAACTA
CAGGCTTTACATATATAACGCCAAAGAGGTCAAAAGGCTTATTAACAAGAATGACCTTCAGAAGCTGCTCAAGCTGGACC
AGCTAAATGTGCAGCGCGCGAGCAAGAAAGCTTTTGCCGACTTCACAGAAGGAGACATCAGGTTTATCCCCACCTACAAG
TTTGACAGCAAAACAGACCGCTGGGACTCCAGCGGCAAGTGCCGGGTCCCCGCGTGGTGTGACAGAATCCTGTGGAAGGG
GACCAACGTGAGTCAGGTCCGCTATCAGAGTCACATGGGGCTAAAAACCAGCGACCACAAACCCGTCAGTTCTCTCTTCC
TTATCGGAGTGAAAATTGTAGATGACAGGAGGTACCAAGAGGTGTTTGAAGACAGTACTCAGCTCATAGACAGAATGGAA
AACTACTTCCTTCCTTCCGTCGTCCTTAGCAGGAGAGATTTCAGGTTTGAAAATGTGAAATTTCGGCAGCTGCAGAAGCA
GAAATTGCAGATCACCAACAATGGGCAGGTTCCCTGCCATTTTTCCTTCGTCTCTAAGCTGGGTGACAAGCAGTACTGCA
AACCGTGGCTTCAGGCTAAGCCCTGTGATGGCTACTTGGAGCCCAATGAGACGGTGGACATTTTCTTGAGTGTCTACGTT
AATAAAGATTCTGTGCCGGTCCTGAGCTCTGGGGAAGATAGTATTAAAGATATTCTCATCCTTCACGTGGATCAAGGCAA
AGATTACTTCCTGACCATCAGCGGCACTTACCTTCGGAGTTGTTGTGGCACATCCCTGGAAACTTTGTGCCAGTTGAGAA
GACCAATCCAAGAAGTTCCTATTTCCAAACTCATAGACTTGGAGATGACTTCTTTGGAGGAGAGTGTTGGTGAAAAGCCC
CTTCAGATTCCCAAGGAACTCTGGCTCTTAGTGGACCACTTATATAAACATGCCTGTGACCAGAAGGATTTGTTCCAGAC
TCCCGGATCACAAAAAGAAGTGCAACAAATTATTGATTGTTTGGATACTAGCATTCTGAAATTAATACCTGGCAGTAATC
ACTCAATAGCTGAGACACTCCTCATCTTCCTGGAAGCCCTGCCAGAGCCCGTTATCTCTTATGAACTATATCAGCGATGC
CTTGACTATTCACACGACCACCGACTCTGCCAGCAAGTGATTTCACACCTTCCACAGTACCACAGAAACGTCTTCTGGTA
TCTGATCGCTTTCCTTCGCGAACTCTTAAGGCACTCTGAAACTAACAACATCACTGCCAATATGCTCGCCAATCTTTTCT
CAAGTCTTCTACTACGGCCTCCACCTAATCTAAAGGCAAAACAGACTCAGAACCACCGGCGTGCTGTCCAGTTTCTCTTG
GGCTTCTTGCTTGGAGGTGATAAAAACTAA

Alignment

ORF - retro_shar_100 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 65.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLEKKRNIHNRQMRTRREPPPPPSH-ISKSFLREKEAAGKDQPKVTNTMRKLFVPTPQTGQREGLIRHI
          MSL.KKR.....QM...R..PPP..........REK.AAG.....VT.T.RKL..P.P..G.R..LIR..
Retrocopy MSLDKKRSAPYHQMKKPRDEPPPIARPLRRELPREKGAAGRGPSRVTSTVRKLLGPNPHPGMRQELIRLV

Parental  LAKREKEYVNIQPFRFFIGTWNVNGQSPDSALEPWLNCDPDPPDIYCLGFQELDLSTEAFFYFESTKEQE
          .AKREKEYVN...FR.F.GTWNVNGQ.PD..LE.WL.CD.DPPDIYCLGFQELDLS.EAFFY.ES..E.E
Retrocopy AAKREKEYVNFRTFRLFAGTWNVNGQPPDCGLELWLSCDRDPPDIYCLGFQELDLSMEAFFYLESAREHE

Parental  WLNSVDRALHYKAKYKKVQLVRLVGMMLLIFAKKDQCKFLHDIVTETVGTGLMGKMGNKGAVAVRFLFHN
          WL.SV..ALH.K.KYKKVQLVRLVGM.LLIFA.K..C....D.VT.TVGTGLMGKMGNKGAVAVRF.FHN
Retrocopy WLASVKQALHAKSKYKKVQLVRLVGMLLLIFARKEHCGHIQDVVTDTVGTGLMGKMGNKGAVAVRFMFHN

Parental  TTFCIVNSHLAAHVEDFERRNQDYKDICSRMSFFVPNQGHLNIMKHDVVIWLGDLNYRLCMPDANEVKML
          T.FC.VNSHLAA..ED.E.RNQDYKDIC.RM.FFVPNQG.LNIMKHDVVIWLGDLNYRL....A.EVK.L
Retrocopy TSFCVVNSHLAAQGEDVEGRNQDYKDICARMNFFVPNQGQLNIMKHDVVIWLGDLNYRLYIYNAKEVKRL

Parental  IHRNELQKLLKLDQLNIQRSHKKAFADFTEGEIGFMPTYKFDPKTDRWDSSGKCRTPAWCDRILWRGSNI
          I..N.LQKLLKLDQLN.QR..KKAFADFTEG.I.F.PTYKFD.KTDRWDSSGKCR.PAWCDRILW.G.N.
Retrocopy INKNDLQKLLKLDQLNVQRASKKAFADFTEGDIRFIPTYKFDSKTDRWDSSGKCRVPAWCDRILWKGTNV

Parental  NQVRYWSHMELKTSDHKPVSSVFLIGVKVVDDRRYRKVFEDSVRIMDRMENDFLPSLELSKREFVFEKVK
          .QVRY.SHM.LKTSDHKPVSS.FLIGVK.VDDRRY..VFEDS....DRMEN.FLPS..LS.R.F.FE.VK
Retrocopy SQVRYQSHMGLKTSDHKPVSSLFLIGVKIVDDRRYQEVFEDSTQLIDRMENYFLPSVVLSRRDFRFENVK

Parental  FRQLQKQKFQVTNNGHVPCHFSFIPKLSDSQYCKPWLRAEPCEGYLEPSETVDISLDVYVSKDSVTILNS
          FRQLQKQK.Q.TNNG.VPCHFSF..KL.D.QYCKPWL.A.PC.GYLEP.ETVDI.L.VYV.KDSV..L.S
Retrocopy FRQLQKQKLQITNNGQVPCHFSFVSKLGDKQYCKPWLQAKPCDGYLEPNETVDIFLSVYVNKDSVPVLSS

Parental  GEDKIEDILVLHLDRGKDYFLTISGNYLPSCFGTSLEALCHMKRPIREVPVTKLIDLGEDTFVEKESPLL
          GED.I.DIL.LH.D.GKDYFLTISG.YL.SC.GTSLE.LC...RPI.EVP..KLIDL.E.T..E......
Retrocopy GEDSIKDILILHVDQGKDYFLTISGTYLRSCCGTSLETLCQLRRPIQEVPISKLIDL-EMTSLEESVGEK

Parental  PLAAPSE
          PL..P.E
Retrocopy PLQIPKE

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_100 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	ENSMODG00000013199	1 retrocopy	retro_mdom_213,
Sarcophilus harrisii	ENSSHAG00000014095	1 retrocopy	retro_shar_100 ,