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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggctagtacaatggaacagtttctttagttgtttagctgtatggtttcagctttgcgttactaatgttgttctccgtaaacaccaaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGTCAAAGTACTTCGCCTACTTAACGAGGAGCCTGCAAGAGAACCGGAGCTT

Basic information

species Zea mays
transcript GRMZM2G033592_T01
intron # 18
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|211088560|gb|FL435458.1|FL435458
EST:     GATGTGGTATGACAACACTGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|18168609|gb|BM338449.1|BM338449
EST:     GATGTGG--TGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTT-GAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|22549263|gb|BU101464.1|BU101464
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|20803078|gb|BQ294128.1|BQ294128
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|16926650|gb|BM079718.1|BM079718
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|211226693|gb|FL103755.1|FL103755
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|26559626|gb|CA831861.1|CA831861
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCT
EST: gi|26456384|gb|CA827967.1|CA827967
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACT
EST: gi|22818916|gb|BU499006.1|BU499006
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCA-GGGC
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGC
EST: gi|78544545|gb|DV622043.1|DV622043
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|87157223|gb|DY402012.1|DY402012
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|5597242|gb|AI891235.1|AI891235
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|5871470|gb|AW017941.1|AW017941
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|78021173|gb|DV489560.1|DV489560
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
EST: gi|32864143|gb|CF003825.1|CF003825
EST:     GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG                         CCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT
genomic: GATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGT

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), 48 (downstream exon)
Score: 56

TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGTCAAAGTACTTCGCCTACTTAACGAGGAGCCTGCAAGAGAACCGGAGCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGTCAAAGTACTTCGCCTACTTAACGAGGAGCCTGCAAGAGAACCGGAGCTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 162

TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGTCAAAGTACTTCGCCTACTTAACGAGGAGCCTGCAAGAGAACCGGAGCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACGgtaatggcta ... aaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGTCAAAGTACTTCGCCTACTTAACGAGGAGCCTGCAAGAGAACCGGAGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtttcagctttgcgttactaatgttgttctccgtaaacaccaaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGTCAAAGTACTTCGCCTACTTAACGAGGAGCCTGCAAGAGAACCGGAGCTT
                   tactaat  putative branch site (score: 79)
                  ttactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggctagtacaatggaacagtttctttagttgtttagctgtatggtttcagctttgcgttactaatgttgttctccgtaaacaccaaatcaccagCCAATAAGTTTTGGAGCGGGCTGCTGAAGAGCTACTACCTTCCAAGGGCGTCAAAGTACTTCGCCTACTTAACGAGGAGCCTGCAAGAGAACCGGAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT