RetrogeneDB ID: retro_shar_94

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861646.1:2201708..2202869(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000016502
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017173
• Aliases: None
• Description: None

Sequence

>retro_shar_94
ATGGAGACCCTGAGCAGAGCCCGGACGCTGAGCCGGGCACTGGGGGTAGCCACGAAGCTTGGGGCCTGGAGGAGCCTGAT
CACCACTGCCGCCACACACCCCATCCACAGACTCGCGGTGGAAGAGGGCAAGGCGGAGGGCGTCTATCCGGTCACCATGG
TGCCCGGCGACGGGGTGGGGCCTGAGCTCATGCTGGCTGTCAAAGAAGTCTTTAAGGCGGCCAGGGTGCCGGTGAAATTT
CAGGAGCATCATCTGAGCGAAGTGCAGAATTTTGCCTCAGAAGAAAAACTGGAGCAAGTGCTGAACTCCATAAAGAAAAA
CAAGGTGGCCATCAGTGGGAAAATCCACTCCCCGATGGACACAACCTACACTGGGGACCTGACTTCGTATAACATGCAGC
TCAGGCGCAAGCTGGACCTGTTCGCCAACGTGGTCCACGTCCAGAGCCTCCCGGGCTATAAGACTCGGCATAACAACCTG
GACTTGGTGATCATCCGCGAGCAGACGGAGGGCGAATACAGCTCGCTGGAGCACGAGAGCGTCAGGGGCGTGATTGAGTG
TTTGAGGATCATCACGCGCGTCAAGTCGGAGCGCATCGCCAAGTTTGCCTTTGACTACGCCACCACGAAGGGCCGCGGGA
AGGTCACGGCGGTGCACAAGGCCAACATCATGAAGCTGGGCGACGGGCTCTTCCTGAAGTGCTGCGAGGAGGTGGCCGGG
CTCTACCCCAAGATCAGGTTCGAGACCATGATCATAGACAACTGCTGCATGCAGCTGGTGCAGAACCCGTACCAGTTCGA
CGTGCTCGTGATGCCCAATCTCTACGGGAACATCATTGACAACCTGGCGGCGGGCCTGGTGGGGGGCGCGGGCGTGGTCC
CTGGCGAGAGCTACAGCGATGAGTGCGCCGTTTTTGAAACCGGAGCCAGACACCCGTTTGCTGAGGCGGTGGGCAGGAAC
ATTGCCAACCCCACTGCCATGCTGCTGTCTTCCAGCAACATGCTGAAGCACCTCAGCCTGGACTACCACTCCAGAATGAT
CGCCGAGGCTGTAAAGAAGGTGATCAGAGTGGGCAAAGTTCGGACGTCGGACATGGGCGGCTACAGCTCCACCACCGAGT
TCATCAAGTCTGTCATTAGCCACCTTCAGCCGCCTTATGGG

Alignment

ORF - retro_shar_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 99.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATLSGVRALRRVRPWRSRPAGGGGTASTAAARASPRSAVDDVRVEGAFPVTMLPGDGVGPELMHAVKEV
          M.TLS..R.L.R................TAA.....R.AV.....EG..PVTM.PGDGVGPELM.AVKEV
Retrocopy METLSRARTLSRALGVATKLGAWRSLITTAATHPIHRLAVEEGKAEGVYPVTMVPGDGVGPELMLAVKEV

Parental  FKAANVPVEFQEHHLSEVQNMASEEKLEQVLSSMKENKVAIIGKIHTPMDTEYKGDLASYDMRLRRKLDL
          FKAA.VPV.FQEHHLSEVQN.ASEEKLEQVL.S.K.NKVAI.GKIH.PMDT.Y.GDL.SY.M.LRRKLDL
Retrocopy FKAARVPVKFQEHHLSEVQNFASEEKLEQVLNSIKKNKVAISGKIHSPMDTTYTGDLTSYNMQLRRKLDL

Parental  FANVVHVKSLPGYKTRHNNLDLVIIREQTEGEYSSLEHESARGVIECLKIVTRAKSQRIAKFAFDYATKK
          FANVVHV.SLPGYKTRHNNLDLVIIREQTEGEYSSLEHES.RGVIECL.I.TR.KS.RIAKFAFDYAT.K
Retrocopy FANVVHVQSLPGYKTRHNNLDLVIIREQTEGEYSSLEHESVRGVIECLRIITRVKSERIAKFAFDYATTK

Parental  GRGKVTAVHKANIMKLGDGLFLQCCEEVAELYPKIKFETMIIDNCCMQLVQNPYQFDVLVMPNLYGNIID
          GRGKVTAVHKANIMKLGDGLFL.CCEEVA.LYPKI.FETMIIDNCCMQLVQNPYQFDVLVMPNLYGNIID
Retrocopy GRGKVTAVHKANIMKLGDGLFLKCCEEVAGLYPKIRFETMIIDNCCMQLVQNPYQFDVLVMPNLYGNIID

Parental  NLAAGLVGGAGVVPGESYSAEYAVFEMGARHPFAQAVGRNIANPTAMLLSSSNMLRHLKGSLEYHSNMIA
          NLAAGLVGGAGVVPGESYS.E.AVFE.GARHPFA.AVGRNIANPTAMLLSSSNML.HL..SL.YHS.MIA
Retrocopy NLAAGLVGGAGVVPGESYSDECAVFETGARHPFAEAVGRNIANPTAMLLSSSNMLKHL--SLDYHSRMIA

Parental  EAVKKVIKAGKVRTRDMGGYSTTSDFIKSVISHLHPPHG
          EAVKKVI..GKVRT.DMGGYS.T..FIKSVISHL.PP.G
Retrocopy EAVKKVIRVGKVRTSDMGGYSSTTEFIKSVISHLQPPYG

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_94 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005208	1 retrocopy	retro_mdom_106,
Otolemur garnettii	ENSOGAG00000004684	1 retrocopy	retro_ogar_2890,
Sarcophilus harrisii	ENSSHAG00000017173	1 retrocopy	retro_shar_94 ,
Tupaia belangeri	ENSTBEG00000011579	2 retrocopies	retro_tbel_3404, retro_tbel_4122,