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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACAGCTGTTGCTGTACCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgctgcagtaaaatcttatggttgttttcagtacatagtctatagttctaagatattgtttggttgaagcatcacctccaggtctacctggcca...

Basic information

species Zea mays
transcript GRMZM2G146374_T02
intron # 5
splice site 5'
intron type U2

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|33285799|gb|CF075594.1|CF075594
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|32850027|gb|CD989708.1|CD989708
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|60400981|gb|DN233788.1|DN233788
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|31364283|gb|CD448638.1|CD448638
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|38229847|gb|CF920160.1|CF920160
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCCAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|32911553|gb|CF016365.1|CF016365
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGAC
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGAC
EST: gi|34391369|gb|CF384597.1|CF384597
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|4217768|gb|AI391764.1|AI391764
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|32943661|gb|CF048480.1|CF048480
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|33285782|gb|CF075577.1|CF075577
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|71325319|gb|DR799337.1|DR799337
EST:     TGCAGCACTGACGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|4217837|gb|AI391833.1|AI391833
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|32856672|gb|CD996353.1|CD996353
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|4573150|gb|AI438501.2|AI438501
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|211477511|gb|FL096882.1|FL096882
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|4217951|gb|AI391947.1|AI391947
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|33771123|gb|CF272784.1|CF272784
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|38229799|gb|CF920112.1|CF920112
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|211073944|gb|FL168133.1|FL168133
EST:     TGCAACACTGATGATGCGTGATCGGCCTGTTTATGACCAGAAAGTGAAGG                         A-TATTGTGAAAAGTATGCTAAACCAGAAGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|71432138|gb|DR813188.1|DR813188
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|71769127|gb|DR967064.1|DR967064
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|83278687|gb|DV942695.1|DV942695
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|211477514|gb|FL096885.1|FL096885
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|4217937|gb|AI391933.1|AI391933
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|32856738|gb|CD996419.1|CD996419
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|211536461|gb|FL178300.1|FL178300
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         A-TNATTGTGAAAAGTATGCTAAACCCAGAG-ACGCTGGCATCACCCCGGA
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAAT-ATTGTGAAAAGTATGCTAAACC-AGAGGACGCTGGCATCACCCCGGA
EST: gi|16925233|gb|BM078301.1|BM078301
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|211073943|gb|FL168132.1|FL168132
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|32912993|gb|CF017805.1|CF017805
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGNGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|78082922|gb|DV511315.1|DV511315
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|4217817|gb|AI391813.1|AI391813
EST:     TGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAACCCAGAGGACGCTGGCATCTCCCCGGAAG
genomic: TGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|211536459|gb|FL178298.1|FL178298
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCAC
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCAC
EST: gi|211073941|gb|FL168130.1|FL168130
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
EST: gi|211477513|gb|FL096884.1|FL096884
EST:     TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAG                         AATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG
genomic: TGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAG

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: 461

CCACAGCTGTTGCTGTACCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAGACAAGTCCAGTGACGAAGAGCTTAGCGATGACGACGACGACGACAACGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1200

CCACAGCTGTTGCTGTACCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAGACAAGTCCAGTGACGAAGAGCTTAGCGATGACGACGACGACGACAACGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 952

CCACAGCTGTTGCTGTACCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAGACAAGTCCAGTGACGAAGAGCTTAGCGATGACGACGACGACGACAACGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 796

CCACAGCTGTTGCTGTACCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgct ... gcttctgcagAATATTGTGAAAAGTATGCTAAACCAGAGGACGCTGGCATCACCCCGGAAGACAAGTCCAGTGACGAAGAGCTTAGCGATGACGACGACGACGACAACGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACAGCTGTTGCTGTACCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGATCGGCCTGTTTATGAACAGAAAGTGAAAGgtacagtgctgcagtaaaatcttatggttgttttcagtacatagtctatagttctaagatattgtttggttgaagcatcacctccaggtctacctggcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagtaaaa