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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgacatctagcttattaggacccccaaataatttatgtatatttttacattttctggttagtgaccagcagcttaattataacacggcttttattttggtaatttatcttactaattcttgttttccatcgaacag

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g58580.1 (Oryza sativa), 5'ss of exon 9
GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgacatctagcttattaggac-ccccaaataatttatgtatatttttacattttctggttagtgaccagcagcttaattataacacggcttttattttggtaatttatcttactaattcttgttttccatcgaacag
|| || || ||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||   |||   |    |  |    |    || ||||||| |  ||    ||||| |   ||     ||   |||  | ||  ||      | |  ||||                                      
GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGACAAAACCTACAAGgtgatatgtactctttttagcaaaaaagtgcttcctactttatgtgtggttaagtattttatccata-----caat-gctagaataacaccttatatatgctttgc-------------------------------------

upper sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA18G46390.1 (Glycine max), 5'ss of exon 10
-GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgacatctagcttattaggacccccaaataatttatgtatatttttacattttctggttagtgaccagcagcttaattataacacggcttttattttggtaatttatcttactaattcttgttttccatcgaacag
 || || || ||||||||||||||||| || ||| ||||||||||||| |  ||  | ||||| || ||||| || || || || |||||||| |    | |   || |||| | |                 ||| ||||||  | | ||         | || || ||||   ||     | ||    |  |    |  |||    ||| ||| ||| ||           
GGTTTTCCCTCAAGGTTGGGACAAAACATACTGCCTGAGATATCTTGATGGTTTCAATGAAATTCACTTCTTCGGTGACAAAACTTACAAggttagtccata---agtttatcatgga---------------gtacatttttggagtatcaa-------atcaacatcttagacattttctgcctcccttcat----acatat---gctagttcgtgtatt-----------

upper sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 10
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 5'ss of exon 9
GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgacatctagcttattaggacccccaaataatttatgtatatttttacattttctggttagtgaccagcagcttaattataacacggcttttattttggtaatttatcttactaattcttgttttccatcgaacag
|| || |||||||| |||||||| || || ||||||||||| ||||| || ||||  |||||||| |||||||| ||||| || ||| |||| |    || | |   ||   |  |  |    ||   ||    |  |    ||      || ||         ||  ||  |     || |  || ||||| | |  | || |  |                         
GTTTTCCCCCAAGGCTGGGACAAGACATACTGCTTGAGATACCTTGATGATTTTCCTGAAATCCACTTCTTTGGCGATAAAACATACGAGgtaa----actttttattttgcacaattc----atctcttgcaaaagtccccaccaaacttgtttgac------catgttgttctcttcatgctttgtattt-gct--tctacccca-------------------------

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|6020771|gb|AW065579.1|AW065579
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|5871671|gb|AW018142.1|AW018142
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|86471496|gb|DY237866.1|DY237866
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|85151824|gb|DW587525.1|DW587525
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATCCA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|76011520|gb|DT938690.1|DT938690
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|5361143|gb|AI795758.1|AI795758
EST:     ATTTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|211038831|gb|FL468651.1|FL468651
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|45846830|gb|CN070773.1|CN070773
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|32919709|gb|CF024521.1|CF024521
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|14700950|gb|BI233368.1|BI233368
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|5871104|gb|AW017545.1|AW017545
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|148947872|gb|EC893365.2|EC893365
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|76280415|gb|DV019983.1|DV019983
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGGCA-TGACTATGAGATATTTGAATCTGAAA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGG-CAATGACTATGAGATATTTGAATCTGAAA
EST: gi|40302745|gb|CK347132.1|CK347132
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|32909183|gb|CF013995.1|CF013995
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
EST: gi|32909184|gb|CF013996.1|CF013996
EST:     ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG                         GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA
genomic: ATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACA

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), 49 (downstream exon)
Score: 70

GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 154

GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 68

GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 129

GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgac ... catcgaacagGGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAGgtgatatgacatctagcttattaggacccccaaataatttatgtatatttttacattttctggttagtgaccagcagcttaattataacacggcttttattttggtaatttatcttactaattcttgttttccatcgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA