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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatctctagctaacgtatactgtttctccttaaaatttagagtatttggtctaattttttttggcttttttgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG

Basic information

species Zea mays
transcript GRMZM2G461793_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g16950.3 (Oryza sativa), 3'ss of exon 4
gtatgcatctctagctaacgtatactgtttctccttaaaatttagagtatttggtctaattttttttggcttttttgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG
|||||||  || ||||     || |  | |     | || |||    | ||  |||| ||   || |   | |||  | ||  ||||||||||||| ||| ||||||||||||| || || ||||| ||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||
gtatgcacttcgagctttgtcattcgatctggatgtgaactttta--ttttaagtctcatagcttgtctttctttcattatgtagGAATTTTGGCCCAAGTTACTTGTGCACAAAATTAAGCAGCGCCTGACAAAAATGACTCAGTATCGGATAAGAATGAGGAAGCTTCAACTGAAAGTGAG

upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g17040.1 (Oryza sativa), 3'ss of exon 3
gtatgcatctctagctaacgtatactgtttctcctta-----aaatttagagtatttggtctaatt-----ttttttggcttttttgtcatta---agGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG
|||||||  || |||  || |||  |||   |||  |     |  |  |   || || |||| ||      | |||     |||   |||||    ||||||||||||| ||| |||||||||||||||| || ||||| ||||||||||||||||| ||||| |||||||||||||| |||| ||||||||||||
gtatgcacttcgagcgtacatattttgtcattccccatctggatgtcaactttacttagtctcatagcttgtctttcactctttccttcattgtgtagGAATTTTGGCCCAAGTTACTTGTGCACAAGATTAAGCAGCGCCTGACAAAAATGACTCAGTATCGGATAAGAATGAGGAAGCTTCGACTGAAAGTGAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|93012902|gb|EB638422.1|EB638422
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|71330256|gb|DR801876.1|DR801876
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|148939429|gb|EC883983.2|EC883983
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|31355775|gb|CD440132.1|CD440132
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|76932105|gb|DV172945.1|DV172945
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|211373401|gb|FL472199.1|FL472199
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|29130836|gb|CB381540.1|CB381540
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|148946083|gb|EC891379.2|EC891379
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|91872818|gb|EB402775.1|EB402775
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|148987550|gb|EE031415.2|EE031415
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|94477914|gb|EB706872.1|EB706872
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|211360103|gb|FL362300.1|FL362300
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|71322072|gb|DR797726.1|DR797726
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|31355774|gb|CD440131.1|CD440131
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
EST: gi|148953458|gb|EE152961.2|EE152961
EST:     AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTT                         GAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA
genomic: AACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 319

GAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 394

GAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

GAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGAAGTCATAAACAAACATCTTgtatgcatct ... tgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccttaaaatttagagtatttggtctaattttttttggcttttttgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG
                       gtctaat  putative branch site (score: 327)
                             ttttttttggcttttt  CT-rich tract
     taaaatttagagtatt  TA-rich tract