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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggattgctagctagtataatattctggtgtaatgcttgtgctatgaaagcttgattgaaatagcaccctgtcttttctgactgaagttattgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG

Basic information

species Zea mays
transcript GRMZM2G058407_T01
intron # 2
splice site 3'
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|44682050|gb|CK787098.1|CK787098
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186460|gb|FL239191.1|FL239191
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|32863264|gb|CF002946.1|CF002946
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211188850|gb|FL239192.1|FL239192
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|32936820|gb|CF041639.1|CF041639
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGTAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186450|gb|FL239181.1|FL239181
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|45213689|gb|CK849962.1|CK849962
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186452|gb|FL239183.1|FL239183
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|32937577|gb|CF042396.1|CF042396
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186458|gb|FL239189.1|FL239189
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186455|gb|FL239186.1|FL239186
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|32864829|gb|CF004511.1|CF004511
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGA-C-CGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|116818620|gb|EC861668.1|EC861668
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186449|gb|FL239180.1|FL239180
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|32936664|gb|CF041483.1|CF041483
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|32906973|gb|CF011786.1|CF011786
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186448|gb|FL239179.1|FL239179
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186459|gb|FL239190.1|FL239190
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186451|gb|FL239182.1|FL239182
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186454|gb|FL239185.1|FL239185
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|44681672|gb|CK786720.1|CK786720
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|33942654|gb|CF349254.1|CF349254
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186453|gb|FL239184.1|FL239184
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211089528|gb|FL476391.1|FL476391
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186456|gb|FL239187.1|FL239187
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|211186447|gb|FL239178.1|FL239178
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
EST: gi|76292026|gb|DV031594.1|DV031594
EST:     ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAG                         TGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG
genomic: ATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAG

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), 48 (downstream exon)
Score: 85

ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 92

ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

ACCCGCTACGTGATGAAGTATCGGCACTGCGAGGGGAAGCTCGTGCTCAAGGTCACTGATGACCGCGAGgtactacctt ... ttgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaagcttgattgaaatagcaccctgtcttttctgactgaagttattgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG
                              ttctgac  putative branch site (score: 219)
         attgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggattgctagctagtataatattctggtgtaatgcttgtgctatgaaagcttgattgaaatagcaccctgtcttttctgactgaagttattgcctgcagTGCTTGAAATTCAAGACAGATCAAGCTCAGGACGCAAAGAAGATGGAGAAGCTCAACAACATCTTTTTTGCTCTGATGACTCGTGGGCCTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - -tgctagc
- - - - - - - - - - - -tctggtg
- - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgattg