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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtaactgttggcgctcattttttttttctctctctcagacaccatttaactgaagcatcaaactttccatggctcataatcactatgcttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA

Basic information

species Zea mays
transcript GRMZM2G017941_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017941_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------------------------gtaggtaactgttg-gcgc-tcattttttttttctctctctcagacaccatttaactgaa-gcatcaaactttccatg-gctcataatcactatgct-tgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA
                                                                                   |   |||| | ||  ||| ||    | ||| | |||| |  ||     || |||||||| || | ||  |||| |   ||| ||||    |||| | | ||| ||  ||| ||  ||   || |||||||| ||||||||||||||| || |||  ||||| ||||| ||| ||||| ||||||||||||| || ||  ||||||
gtattcataattgctcttcttttgcccttcccccatatttgtatctcccctttttcagataatggattaaaccgacctcgatatccataacggatgtacgcatccacatatttgtatctcccgtagttgttatataactgaaagcttaaagatttctaaatgcttataacatatatgttctttactagAACTCGTTTGCAAGCTCCGAGTTTTCGATGGCATTCCCCTACATTGCCATGTCAGATGATGACAAATTGGAGAAGTCATTGCTATCTGGGTTTGCTGAGA

upper sequence: GRMZM2G017941_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g03060.1 (Oryza sativa), 3'ss of exon 5
----------gtaggtaactgttggc-gctcattttttttttctctctctcagacaccatttaactgaagcatcaa--actttccatggctcataatcactatgct-tgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA
            |     || ||| |    |   || ||| | | || |  ||     || ||||||||  || ||  | |||  |  ||| |||||  ||||||| | ||| ||  ||||||  ||   || |||||||| |||||||||||||| ||| |||  ||||| ||||| ||| ||||| ||||||||||||| || ||  ||||||
gtattcataatcactcttcttttgtccatcccccttatttgtatttcccctagttgttatataactgaaaaattaaagatttttaaatgcttataatatctatgctctttactagAACTCCTTTGCAAGCTCCGAGTTTTCCATGGCATTCCCCTATGTTGCCATGTCAGATGATGACAAATTGGAGAAGTCATTGCTATCTGGATTTGCTGAGA
















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|211169637|gb|FL169510.1|FL169510
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAG
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAG
EST: gi|149084465|gb|EE173923.2|EE173923
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211171318|gb|FL169524.1|FL169524
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211169635|gb|FL169508.1|FL169508
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCA
EST: gi|149108720|gb|EE292928.2|EE292928
EST:     ACATATCGAAAGATAAGCAAGTTGATCCCGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|71329488|gb|DR801466.1|DR801466
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211169629|gb|FL169502.1|FL169502
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211171321|gb|FL169527.1|FL169527
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATC
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATC
EST: gi|211174667|gb|FL169548.1|FL169548
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211171319|gb|FL169525.1|FL169525
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211171310|gb|FL169516.1|FL169516
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|149013784|gb|EE043248.2|EE043248
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211171315|gb|FL169521.1|FL169521
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTT
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTT
EST: gi|91877946|gb|EB407903.1|EB407903
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211171316|gb|FL169522.1|FL169522
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTT
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTT
EST: gi|31358873|gb|CD443230.1|CD443230
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|93281025|gb|EB673289.1|EB673289
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|78106618|gb|DV525036.1|DV525036
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|101399852|gb|EB821772.1|EB821772
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211172988|gb|FL169531.1|FL169531
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211169634|gb|FL169507.1|FL169507
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGT
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGT
EST: gi|211172990|gb|FL169533.1|FL169533
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATCCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|67024634|gb|CO453383.1|CO453383
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211171320|gb|FL169526.1|FL169526
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211169641|gb|FL169514.1|FL169514
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGA
EST: gi|211174666|gb|FL169547.1|FL169547
EST:     ACATATCGAAAGATAAGCACGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAAAATCAGAGTTTTCCATGGCATTCCCCT
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCT
EST: gi|211171323|gb|FL169529.1|FL169529
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|211171311|gb|FL169517.1|FL169517
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAAT
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAAT
EST: gi|149072392|gb|EE160666.2|EE160666
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
EST: gi|148982778|gb|EE028604.2|EE028604
EST:     ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG                         CTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA
genomic: ACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACA

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: 45 (upstream exon), 43 (downstream exon)
Score: 52

CTACAATCATCAGACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

CTACAATCATCAGACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 125

CTACAATCATCAGACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

CTACAATCATCAGACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAGgtaggtaact ... cttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttaactgaagcatcaaactttccatggctcataatcactatgcttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA
 atttaac  putative branch site (score: 200)
                 aaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtaactgttggcgctcattttttttttctctctctcagacaccatttaactgaagcatcaaactttccatggctcataatcactatgcttgtaccagCTCTCCTTCACAGAATCAGAGTTTTCTATGGCATTCCCCTACGTTTCCACATCAGACGATGAGAAACTGGAGGAGTCATTGCTATCAGGCTTCACTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG