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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcaaatcttcatgctgttataactcccattctttctttttgctcttctttttggggcataactgagtaattgaagtgccaggtgttccagaacacccctagttatttgtttttttgtaaagcaatgtataaataggaaatgtcctgtattcgtaatatgcctactacaagtgttttttcctttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTCCACGTTTGAAAGCATTCTCAGATTGGATTCTTAAAGCAATGGCTTTAGG

Basic information

species Zea mays
transcript GRMZM2G127739_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127739_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g40190.1 (Oryza sativa), 3'ss of exon 5
gtatgatcaaatcttcatgctgttataactcccattctttctttttgctcttctttttggggcataactgagtaa-ttgaagtgccaggtgttccagaacacccctagttatttgtttttttgtaaagcaatgtataaataggaaatgtcctgtattcgtaatatgcctactacaagtgttttttcctttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTCCACGTTTGAAAGCATTCTCAGATTGGATTCTTAAAGCAATGGCTTTAGG
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gtatgacag-----tcgtattattatg-----------ttcttttggctatccaccttaattctttgctgcataaattcacatatttatatcagcaggagacttgcaattgtttgatttt----agtgaaacatatagactgctagcctctt----ccacagaccatctagaatttat-ttttgtgtttcttttgcagGCCATTGTGAACCAGAGCTTTGTAATGACATTACTGAGTACTATATTGCTCCACGCCTGAAAGCATTCTCTGATTGGATTCTAAAAGCTATGGCCATAGG
















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|94473931|gb|EB702889.1|EB702889
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|71763610|gb|DR961547.1|DR961547
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|76017187|gb|DT944357.1|DT944357
EST:     TTAGCTGATAG-AGAAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: TTAGCTGATAGAAG-AAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|78110170|gb|DV528585.1|DV528585
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|94475631|gb|EB704589.1|EB704589
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|71322062|gb|DR797719.1|DR797719
EST:     AAAACCAGTCAGTGTG-CCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: AAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|149070928|gb|EE159335.2|EE159335
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|78119468|gb|DV537852.1|DV537852
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCGG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|71308379|gb|DR790418.1|DR790418
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTCCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|71760704|gb|DR958641.1|DR958641
EST:     CCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: CCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|71328662|gb|DR801008.1|DR801008
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|74241916|gb|DT649830.1|DT649830
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|71758063|gb|DR956000.1|DR956000
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|6021458|gb|AW066386.1|AW066386
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATCTGACG
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACG
EST: gi|74237568|gb|DT645482.1|DT645482
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|148929836|gb|EE285518.2|EE285518
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|149075131|gb|EE163624.2|EE163624
EST:     AGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: AGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|149100969|gb|EE187066.2|EE187066
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|149061146|gb|EE157406.2|EE157406
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|86469211|gb|DY235581.1|DY235581
EST:     ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         GGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: ATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
EST: gi|149109394|gb|EE293282.2|EE293282
EST:     TC-TTAGCTGATAGNAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTG                         AGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC
genomic: TCTTTAGCTGATAG-AAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTC

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: 263

TACAACTACCTTGGCATATTGCTTGAAGGGCGTGAGCGGTTTGAAGAGGAATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTCCACGTTTGAAAGCATTCTCAGATTGGATTCTTAAAGCAATGGCTTTAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 134

TACAACTACCTTGGCATATTGCTTGAAGGGCGTGAGCGGTTTGAAGAGGAATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTCCACGTTTGAAAGCATTCTCAGATTGGATTCTTAAAGCAATGGCTTTAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 96

TACAACTACCTTGGCATATTGCTTGAAGGGCGTGAGCGGTTTGAAGAGGAATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTCCACGTTTGAAAGCATTCTCAGATTGGATTCTTAAAGCAATGGCTTTAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 131

TACAACTACCTTGGCATATTGCTTGAAGGGCGTGAGCGGTTTGAAGAGGAATCTTTAGCTGATAGAAGAAAAACCAGTCAGTGTGACCCTTCTAGCTCTGgtatgatcaa ... ttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTCCACGTTTGAAAGCATTCTCAGATTGGATTCTTAAAGCAATGGCTTTAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtcctgtattcgtaatatgcctactacaagtgttttttcctttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTCCACGTTTGAAAGCATTCTCAGATTGGATTCTTAAAGCAATGGCTTTAGG
                                  tgttttttcctttttc  CT-rich tract
                                  tgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatcaaatcttcatgctgttataactcccattctttctttttgctcttctttttggggcataactgagtaattgaagtgccaggtgttccagaacacccctagttatttgtttttttgtaaagcaatgtataaataggaaatgtcctgtattcgtaatatgcctactacaagtgttttttcctttttctgcagGGTGTTGTGAACCTGGATTATGTGACGAAGTCACTGAGTACTCCCTTATTCCACGTTTGAAAGCATTCTCAGATTGGATTCTTAAAGCAATGGCTTTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA