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1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaatcgagagaatacttcactgctaccatctcctcttgctcaaaaaaaaaaaaaaagataaagagttgtactcagcgtgacgtttgttttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCAAGGGTGCGGCACGCGGGCTAGCGCACCTTCACGAGTGCAGCCCACGCCG

Basic information

species Zea mays
transcript AC235540.1_FGT002
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235540.1_FGT002 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g19490.1 (Oryza sativa), 3'ss of exon 1
ttaaaatcgagagaatacttcactgctaccatctcctcttgctcaaaaaaaaaaaaaaagataaagagttgtact-cagcgtgacgtttgttttc-ctgcagGCCGGTCCGGTCAGC---CAAGCCTATCATGGACCCTACGGCTGCGGATCGCCAAGGGTGCGGCACGCGGGCTAGCGCACCTTCACGAGTGCAGCCCACGCCG
  ||  | |    |||       |  | | |  |  | ||  | |    || ||       |      | | ||    |  ||| ||   | | | ||||||| ||||| || |||    | |  || || ||| |  | |||||||||||||||||||| ||||| |||||||| |||||||| |||||||||||||| ||   
-aaatgttggttaaatctgatgttttttcgaagtagt-ttaatgatcctaagaatttttcttcttctttgggacggtgggatgatgtggttgtgcactgcagGGCGGTCGGGGCAGGCGGCGACGCTGTCGTGGTCGGTGCGGCTGCGGATCGCCAAGGGCGCGGCGCGCGGGCTGGCGCACCTCCACGAGTGCAGCCCGCG---
















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|148961050|gb|EE011752.2|EE011752
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|78123896|gb|DV542280.1|DV542280
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149105987|gb|EE291625.2|EE291625
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|148936097|gb|EC880160.2|EC880160
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149080128|gb|EE169149.2|EE169149
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149100352|gb|EE186422.2|EE186422
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149112484|gb|EE295355.2|EE295355
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|94478489|gb|EB707447.1|EB707447
EST:     TCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: TCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|88753223|gb|DY537364.1|DY537364
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149108371|gb|EE292709.2|EE292709
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|148983413|gb|EE029411.2|EE029411
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149082704|gb|EE171921.2|EE171921
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|89248631|gb|DY620417.1|DY620417
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|148928477|gb|EE285292.2|EE285292
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149065667|gb|EE286787.2|EE286787
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|91876526|gb|EB406483.1|EB406483
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149043941|gb|EE047420.2|EE047420
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149105988|gb|EE291626.2|EE291626
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|148973174|gb|EE024247.2|EE024247
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|149098398|gb|EE184375.2|EE184375
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|148970814|gb|EE021577.2|EE021577
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
EST: gi|148969189|gb|EE019935.2|EE019935
EST:     CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCG                         GCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA
genomic: CGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCA

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: 46 (upstream exon), 35 (downstream exon)
Score: 9

CCCAACATCGTGAGGCTGCGCGCCTACTACTGGTCCGCCGACGAGAAGCTCGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCAAGGGTGCGGCACGCGGGCTAGCGCACCTTCACGAGTGCAGCCCACGCCG


Block sizes: 44 (upstream exon), 35 (downstream exon)
Score: 12

CCCAACATCGTGAGGCTGCGCGCCTACTACTGGTCCGCCGACGAGAAGCTCGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCAAGGGTGCGGCACGCGGGCTAGCGCACCTTCACGAGTGCAGCCCACGCCG


Block sizes: 36 (upstream exon), 19 (downstream exon)
Score: 4

CCCAACATCGTGAGGCTGCGCGCCTACTACTGGTCCGCCGACGAGAAGCTCGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCAAGGGTGCGGCACGCGGGCTAGCGCACCTTCACGAGTGCAGCCCACGCCG


Block sizes: 49 (upstream exon), 20 (downstream exon)
Score: 9

CCCAACATCGTGAGGCTGCGCGCCTACTACTGGTCCGCCGACGAGAAGCTCGTTATCACGGATTTCGTCAACAACGGCAACCTCGCGACGGCGTTGCGCGgtgagtgcca ... tttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCAAGGGTGCGGCACGCGGGCTAGCGCACCTTCACGAGTGCAGCCCACGCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaaaaaaaagataaagagttgtactcagcgtgacgtttgttttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCAAGGGTGCGGCACGCGGGCTAGCGCACCTTCACGAGTGCAGCCCACGCCG
                                        tttgttttcct  CT-rich tract
     aaaaaaaaagataaag  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaatcgagagaatacttcactgctaccatctcctcttgctcaaaaaaaaaaaaaaagataaagagttgtactcagcgtgacgtttgttttcctgcagGCCGGTCCGGTCAGCCAAGCCTATCATGGACCCTACGGCTGCGGATCGCCAAGGGTGCGGCACGCGGGCTAGCGCACCTTCACGAGTGCAGCCCACGCCG

- - - - - - - - - - - ctgctac
- - - - - - - - - - - - - - - - - - -cttgctc
- - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaaga