RetrogeneDB ID: retro_shar_90

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850687.1:2558..4148(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000000656
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000010300
• Aliases: None
• Description: None

Sequence

>retro_shar_90
TTGACCAAAACAGCCAGCGAATTAGCATTCACTATTCAGAAACATCAGCTGTTTGCTGCTATGGCCGACACCTTTCTGGA
ACATATGTGTCGTTTGGATATCGACTCAGAGCCCATTGTTGCCCGAAAGACTGGAATCGTCTGCACCATTGGCCCAGCCT
CCCGATCTGTGGACAAGCTAAAAGAAATGATAGCAGCTGGAATGAATGTGGCTCGTCTAAACTTCTCCCATGGAACTCAT
GAGTACCATTCAGAAACTATCAAAAATGTGCGCACAGCTACAGAAAACTTTTCTTCTAATCCTGTTTATTACCGGCCCAT
TGCTATAGCCTTGGACACCAAAGGACCAGAGATCCGGACAGGACTCATCAAGGGTAGTGGCACAGCTGAAGTGGAGCTAA
AGAAGGGCAGTAATCTCAAAATAACTTTGGATAATGCCTATATGGATAAATGTGATGAAAATGTCCTGTGGGTAGACTAC
AAAAACATTTGCAAGGTGATGAACGTTGGTGGCAAAATCTTTGTGGACAATGGGCTCATTTCTCTTCTTGTAAAGGAGAA
AGGTAAAGATTTCCTTACAACTGAAGTGGAGAATGGTGGTATGCTGGGCAGCCAGAAGGGTGTGAACCTTCCTGGGGCAG
TTGTAGACTTGCCTGCTGTATCTCAGAAGGATATCCAGGATCTACAGTTTGCATTAGAGCAAGAGGTGGATATGATATGC
GCATCTTTCATCAGAAAGGCTGATGATGTTCATGCAGTCAGAGAGGTCCTGGGAGATAAAGGAAGGGACATCAAGATCAT
CAGCAAGATTGAAAACCATGAAGGAGTCCGAAGATTTGATGAGATCCTGGAAGCTAGTGATGGCATCATGGTTGCTCGGG
GGGACCTGGGTATTGAGATCCCAGCAGAAAAAGTCTTTCTTGCCCAGAAGATGATGATTGGAAGATGTAATCGAGTTGGG
AAACCTGTTATTTGTGCCACTCAGATGCTTGAGAGCATGATTAAGAAGCCACGGCCCACACGTGCTGAAGGTAGTGATGT
AGCCAATGCTGTTCTGGATGGAGCCGATTGTATCATGCTTTCTGGAGAGACTGCCAAAGGAGACTATCCAGTAGAAGCTG
TGCGGATGCAACACTTGATAGCTAGGGAGGCTGAAGCAGCCACATACCACCGCCACCTTTTTGAAGGACTTCTTCGATGC
TCAACATGCACAGACACTGCAGAAGCCATGGCAGTGGGTGCAGTAGAGGCTTCTTATAAGTGTTTATCAGCAGCTTTGAT
AGTTCTGACAGAGAGTGGCAAGTCTGCTCATCAGGTGGCCAGGTATCGTCCTAGGATCCCCATCATAGCTGTGACTCGTT
GTGCTCAGGCTGCACGTCAGGCCCATCTTTATCGAGGTGTCTTCCCTGTGCTGTGCAGAGATGCTGTTCATGAATCATGG
GCTGAAGATGTGGATATCAGGGTTAAGTTAGGCATGAATGTTGGCAAAGCTCACGGCTTTTTCAAGAAAGATGATGTGGT
CATTGTCCTAAATGGTTGGCGTCCAGGTCCAGGCTTCACCAACACTATGCGGCTGCTGGCAGTGCCATAA

Alignment

ORF - retro_shar_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSKTASELACTTIQNQQLFAAMADTFLEHMCRLDIDSEPTVARNTGIICTIGPASRSVDKLKEMIAAGMN
          ..KTASELA.T.IQ..QLFAAMADTFLEHMCRLDIDSEP.VAR.TGI.CTIGPASRSVDKLKEMIAAGMN
Retrocopy LTKTASELAFT-IQKHQLFAAMADTFLEHMCRLDIDSEPIVARKTGIVCTIGPASRSVDKLKEMIAAGMN

Parental  VARLNFSHGTHEYHAETIKNVRTATENFTSDPVYYRPIAIALDTKGPEIRTGLIKGSGTAEVELKKGNTL
          VARLNFSHGTHEYH.ETIKNVRTATENF.S.PVYYRPIAIALDTKGPEIRTGLIKGSGTAEVELKKG..L
Retrocopy VARLNFSHGTHEYHSETIKNVRTATENFSSNPVYYRPIAIALDTKGPEIRTGLIKGSGTAEVELKKGSNL

Parental  KVTLDNAYMEKCDENILWVDYKNICKVVDVGGKIFVDDGLISLLVKEKVGQDFLITEVENGGMLGSKKGV
          K.TLDNAYM.KCDEN.LWVDYKNICKV..VGGKIFVD.GLISLLVKEK.G.DFL.TEVENGGMLGS.KGV
Retrocopy KITLDNAYMDKCDENVLWVDYKNICKVMNVGGKIFVDNGLISLLVKEK-GKDFLTTEVENGGMLGSQKGV

Parental  NLPGAAVDLPAVSQKDIQDLQFGLEQGVDMIFASFIRKAADVHAVREVLGEKGRNIKIISKIENHEGVRR
          NLPGA.VDLPAVSQKDIQDLQF.LEQ.VDMI.ASFIRKA.DVHAVREVLG.KGR.IKIISKIENHEGVRR
Retrocopy NLPGAVVDLPAVSQKDIQDLQFALEQEVDMICASFIRKADDVHAVREVLGDKGRDIKIISKIENHEGVRR

Parental  FDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRVGKPVICATQMLESMIKKPRPTRAEGSDVA
          FDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRVGKPVICATQMLESMIKKPRPTRAEGSDVA
Retrocopy FDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRVGKPVICATQMLESMIKKPRPTRAEGSDVA

Parental  NAVLDGADCIMLSGETAKGDYPVEAVRMQHLIAREAEAAIYHTQLFEELRRLAPITKDPTEAAAVGAVEA
          NAVLDGADCIMLSGETAKGDYPVEAVRMQHLIAREAEAA.YH..LFE.L.R....T.D..EA.AVGAVEA
Retrocopy NAVLDGADCIMLSGETAKGDYPVEAVRMQHLIAREAEAATYHRHLFEGLLRCSTCT-DTAEAMAVGAVEA

Parental  SFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRCAQAARQAHLYRGVFPVLCKDAVHESWAEDVDLR
          S.KC.S.A.IVLT.SG.SAHQVARYRPR.PIIAVTRCAQAARQAHLYRGVFPVLC.DAVHESWAEDVD.R
Retrocopy SYKCLSAALIVLTESGKSAHQVARYRPRIPIIAVTRCAQAARQAHLYRGVFPVLCRDAVHESWAEDVDIR

Parental  VNLAMKVGKARGFFKKDDVVIVLNGWRPGPGFTNTMRVLPVP
          V.L.M.VGKA.GFFKKDDVVIVLNGWRPGPGFTNTMR.L.VP
Retrocopy VKLGMNVGKAHGFFKKDDVVIVLNGWRPGPGFTNTMRLLAVP

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_90 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 13 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013504	1 retrocopy	retro_chof_1430,
Callithrix jacchus	ENSCJAG00000018473	1 retrocopy	retro_cjac_236,
Felis catus	ENSFCAG00000000653	1 retrocopy	retro_fcat_105,
Homo sapiens	ENSG00000067225	2 retrocopies	retro_hsap_210, retro_hsap_3418,
Gorilla gorilla	ENSGGOG00000005062	1 retrocopy	retro_ggor_281,
Macropus eugenii	ENSMEUG00000004506	3 retrocopies	retro_meug_1482, retro_meug_2043, retro_meug_912,
Macaca mulatta	ENSMMUG00000023454	1 retrocopy	retro_mmul_183,
Mus musculus	ENSMUSG00000032294	8 retrocopies	retro_mmus_1402, retro_mmus_1678, retro_mmus_1754, retro_mmus_2065, retro_mmus_2066, retro_mmus_2636, retro_mmus_3509, retro_mmus_854,
Nomascus leucogenys	ENSNLEG00000013869	3 retrocopies	retro_nleu_1859, retro_nleu_2319, retro_nleu_2716,
Pongo abelii	ENSPPYG00000006613	3 retrocopies	retro_pabe_2834, retro_pabe_3645, retro_pabe_429,
Pan troglodytes	ENSPTRG00000007246	2 retrocopies	retro_ptro_2322, retro_ptro_335,
Rattus norvegicus	ENSRNOG00000011329	6 retrocopies	retro_rnor_1120, retro_rnor_2050, retro_rnor_2253, retro_rnor_2703, retro_rnor_515, retro_rnor_830,
Sarcophilus harrisii	ENSSHAG00000010300	1 retrocopy	retro_shar_90 ,