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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcgagacaaacacactatcatgtccagcatatctaaacacgcaacagagaagttctgaatcttattgcgacctgacgattcttctgtag

Basic information

species Zea mays
transcript GRMZM2G023392_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023392_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g44560.1 (Oryza sativa), 5'ss of exon 2
TGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcgagacaaacacactatcatgtccagcatatctaaacacgcaacagagaa---gttctgaatcttattgcgacctgacgattcttctgtag
|||||| | |||||||||||||||||| ||||||||||||||  | ||| |||| |  ||||| |||||  |||||   ||||| ||||||||||| |||||| |   | | |   |   || |  ||| ||| ||  | | |||  |  ||| | |     |||| ||| || |  | | |||| ||| ||| | |||
TGGTGGGTACATGGTAGCATTTGCCGGTAGGAAGTATGCAGCCCGGTCTGTTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCTTCACCCTGgtatggaaccaaa--gatgtaccactatgcccatcacctatcaacttgtgacacaaagaatattcttaatgttgtctccatctgatgatacttgtctag
















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|76285613|gb|DV025181.1|DV025181
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|76281064|gb|DV020632.1|DV020632
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|211198227|gb|FL002575.1|FL002575
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|76016614|gb|DT943784.1|DT943784
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|211198221|gb|FL002569.1|FL002569
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCCAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|149087946|gb|EE287203.2|EE287203
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|8665537|gb|BE186353.1|BE186353
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|149087948|gb|EE177188.2|EE177188
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|76281065|gb|DV020633.1|DV020633
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|18178640|gb|BM379850.1|BM379850
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|211198219|gb|FL002567.1|FL002567
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|211307577|gb|FL417513.1|FL417513
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|78111842|gb|DV530239.1|DV530239
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|211014458|gb|FL404245.1|FL404245
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|78105739|gb|DV524157.1|DV524157
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|149076826|gb|EE165479.2|EE165479
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|74232454|gb|DT640368.1|DT640368
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|74240127|gb|DT648041.1|DT648041
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|74232453|gb|DT640367.1|DT640367
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|45847005|gb|CN070948.1|CN070948
EST:     TCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|148959394|gb|EE010767.2|EE010767
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|31353180|gb|CD437537.1|CD437537
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|32870803|gb|CF010485.1|CF010485
EST:     TTCCGATATTTGTATCTAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|78022745|gb|DV491132.1|DV491132
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|101399855|gb|EB821775.1|EB821775
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|211198225|gb|FL002573.1|FL002573
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAAC
EST: gi|116821439|gb|EC864739.1|EC864739
EST:     TTCCGATATTTGTATCCAACACCTCAGTCCCAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTC
EST: gi|76285614|gb|DV025182.1|DV025182
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|211198226|gb|FL002574.1|FL002574
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|148973610|gb|EE024718.2|EE024718
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
EST: gi|101399860|gb|EB821776.1|EB821776
EST:     TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTG                         GTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC
genomic: TTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGAC

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: 108

TGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGACGGCTGTGGCGCTTGCTCCGGCAAGTCGAACTTCGTCTGCCTCGGCAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

TGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGACGGCTGTGGCGCTTGCTCCGGCAAGTCGAACTTCGTCTGCCTCGGCAAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 44

TGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGACGGCTGTGGCGCTTGCTCCGGCAAGTCGAACTTCGTCTGCCTCGGCAAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

TGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCTTCACACTGgtacgattcg ... tcttctgtagGTACTTGAGTTCAACAAAGGCAGACTCCAAAACTTGCACTGGAAGAAGGACGGCTGTGGCGCTTGCTCCGGCAAGTCGAACTTCGTCTGCCTCGGCAAAC