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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggacaaattgccattactcaatcaacataaattcactagttgctagtatcaaattttaccatgtctcttgccacactaattctgaactgtggtatgtactattaatcatgcatgtgcag

Basic information

species Zea mays
transcript GRMZM2G074436_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074436_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g41990.2 (Oryza sativa), 5'ss of exon 3
AGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggacaaattgccattactcaatcaacataaattcactagttgctagtatcaaattttaccatgtctcttgccacactaattctgaactgtggtatgtactattaatcatgcatgtgcag
|||||||||||| ||||||||  |||| ||||||||||| ||||||||||||||||| ||||||||||| |||||||| || || || |||||||||||||| |||||        ||||||||| ||| | | || ||||  | |||   | || |||||||| |||||    ||||  | ||||  | || |         || |  |       ||||||||
AGACCAGAAGACACTTGAAAAGCTGAGAGCTGAGAGGAAGGCCAAGATTGATGAGCTAAAAGAGAGAACTAATTATTACCTCACCCAACAGCTTATTCAGgtgagtgg--------ccattactcgatctatagaagttcagaacttg---gaataaaattttatcatgttatatgcccaattaatagtaaatt--------caccaagacctgcaaatgtgcag
















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|32921707|gb|CF026519.1|CF026519
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|149089324|gb|EE178549.2|EE178549
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|4730506|gb|AI649672.1|AI649672
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|148955777|gb|EC901479.2|EC901479
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|149010193|gb|EE042010.2|EE042010
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|149075912|gb|EE164472.2|EE164472
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|148999505|gb|EE036470.2|EE036470
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|101397837|gb|EB820795.1|EB820795
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|32843641|gb|CD983322.1|CD983322
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCAGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|71439041|gb|DR820091.1|DR820091
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|5928783|gb|AW056075.1|AW056075
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCAGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|76933107|gb|DV173324.1|DV173324
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|71427128|gb|DR808178.1|DR808178
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|67031507|gb|CO460256.1|CO460256
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACCCAACAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCAGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|93282520|gb|EB674784.1|EB674784
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|74239243|gb|DT647157.1|DT647157
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|33100226|gb|CF060186.1|CF060186
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCAGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|71436211|gb|DR817261.1|DR817261
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|149015075|gb|EE044828.2|EE044828
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|78091242|gb|DV519616.1|DV519616
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|148970214|gb|EE021148.2|EE021148
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|32833079|gb|CD972757.1|CD972757
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCAGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|78115258|gb|DV533646.1|DV533646
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|74240884|gb|DT648798.1|DT648798
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|101399969|gb|EB821831.1|EB821831
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|149084452|gb|EE173910.2|EE173910
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|71431983|gb|DR813033.1|DR813033
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|32832044|gb|CD971722.1|CD971722
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACGCAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCAGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|91053445|gb|EB163863.1|EB163863
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAGAGGCTGCAGCAGCTTCTGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA
EST: gi|32833441|gb|CD973119.1|CD973119
EST:     ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAG                         AAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCAGTTTTGGCA
genomic: ATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 104

AGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCATCTAAGCTTGGGGAGGAGACTGGCTTAAAAGTTCATGTTGGAGAAGAAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 68

AGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCATCTAAGCTTGGGGAGGAGACTGGCTTAAAAGTTCATGTTGGAGAAGAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 101

AGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCATCTAAGCTTGGGGAGGAGACTGGCTTAAAAGTTCATGTTGGAGAAGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

AGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggac ... gcatgtgcagAAATATGATCTTGATCCAGCCGCAAAGGCTGCAGCAGCTTCTGTTTTGGCATCTAAGCTTGGGGAGGAGACTGGCTTAAAAGTTCATGTTGGAGAAGAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACCAGAAGACCCTTGAAAAATTGAGGGCTGAGAGGAAAGCCAAGATTGATGAGCTTAAAGAGAGAACAAATTATTATCTAACACAGCAGCTTATTCAGgtaagtggacaaattgccattactcaatcaacataaattcactagttgctagtatcaaattttaccatgtctcttgccacactaattctgaactgtggtatgtactattaatcatgcatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT