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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacatggttgtagttactgctgtcgtttgaaaggatttcaattagtttcattcatacagttacagtagcaagtgccctggttatgcaattttagttgtcagtgaaatatctgtttctgaaagcacttgccattcctttttaatatcag

Basic information

species Zea mays
transcript GRMZM2G075485_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075485_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 5'ss of exon 6
GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaa----cacatg--gttgtagt-tactgctgtcgtttga----aaggatttcaattagtttcattcatacagtta--cagtagcaa-gtgcc---ctggttatgcaattttagtt--gtcagtgaaa--tatctgtttctgaaagcacttgccattcctttttaatat-cag
|||||| ||  |||||||||||||||| |||||||||||||| || ||||| || ||||||||||| ||||| |||| ||||||||||     | |||  ||||   | || |  | || | | |     |  |  |   |   || | ||  |||| | |  |  | |||| |||     ||  | |||| |  | | |    ||  |||||  | |||  |  | |||   ||| ||||| | ||    | |  ||
GCTTTTTTGTTCAATGATTTGCTCAGATCCAAAGCTTGATTCCCATCGCTTTAAAGATATAATTGATGAGGCAATTGCTGAAGgtaaatgattatatgctgttgccatataattttatcatataatattgaatacctttttctattccttttctacaatgaagcgctggcaaagtgtttagcttatcatgctaactcaatctattccctgaaacttctctaatggttaaactcctttccatttccttcccttttgtag

upper sequence: GRMZM2G075485_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacatggttgtagttactgctgtcgtttgaaaggatttcaattagtttcattcatacagttacagtagcaagtgccctggttatgcaattttagttgtcagtgaaatatctgtttctgaaagcacttgccattcctttttaatatcag
|||||||||| ||||| |||||||  | || ||||||||||| ||||| ||||| ||||| || || ||||| ||||  |  ||||  |   |  || | |  |    | |  | |  |   |    |   || |||  | ||    ||       | | ||       | ||||                                                             
GCTTTTCTGCTCAATGCTTTGCTCGAACCCCAAGCTTGATTCGCACCGTTTCAAAGATATTATCGATGAGGCCATTGCAGCGGgtaggcttctctttcttgcaataattcttttgtctataaaacctatccaggttc--tgatttgtttgtgcataccattgtttaacatctgcag------------------------------------------------------------
















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|71757753|gb|DR955690.1|DR955690
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|91870824|gb|EB401103.1|EB401103
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|78074189|gb|DV502623.1|DV502623
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|32845400|gb|CD985081.1|CD985081
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGACTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|32850389|gb|CD990070.1|CD990070
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGACTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|211431464|gb|FL284143.1|FL284143
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|32844155|gb|CD983836.1|CD983836
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGACTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|32845478|gb|CD985159.1|CD985159
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGACTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|60341956|gb|DN208929.1|DN208929
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|78123755|gb|DV542139.1|DV542139
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|78116315|gb|DV534702.1|DV534702
EST:     CGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: CGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|78074190|gb|DV502624.1|DV502624
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|148958293|gb|EC904513.2|EC904513
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|32909541|gb|CF014353.1|CF014353
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG                         GTGAGCTGAAGT
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGT
EST: gi|148958294|gb|EC904514.2|EC904514
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|78117499|gb|DV535886.1|DV535886
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|32945462|gb|CF050281.1|CF050281
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGACTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|32844895|gb|CD984576.1|CD984576
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGACTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|60351082|gb|DN218055.1|DN218055
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGACTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|71772229|gb|DR970166.1|DR970166
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
EST: gi|71435377|gb|DR816427.1|DR816427
EST:     GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG                         GTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG
genomic: GCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAG

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: 411

GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAGGGATGGAGCCACCAACAAATCCGCTAGAGAGGAGAGTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 122

GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAGGGATGGAGCCACCAACAAATCCGCTAGAGAGGAGAGTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 128

GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAGGGATGGAGCCACCAACAAATCCGCTAGAGAGGAGAGTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAGgtaaacacat ... ttaatatcagGTGAGCTGAAGTCAACTAAGGTGTATGAGAAATGGGCTAAAAAGATCTCAGGGATGGAGCCACCAACAAATCCGCTAGAGAGGAGAGTGAA