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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatcagatatatgaaccttctctttcttcctttgtctttgatttatgatttaatcctggaattgttaagaaattttagatacacatgcttatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAGCTGCATCCAGTGCACCTGCTGCTGCCAGCTCCCTTGCTTCATCTACTCT

Basic information

species Zea mays
transcript GRMZM2G136769_T01
intron # 1
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|211048379|gb|FL399864.1|FL399864
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GTGTTGAGACAGATCACANCAATTCACTTGGTGCGTGGTGTTGCCCCACCA
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACA-CAATTCACTTGGTGCGTGGTGTTGCCCCACCA
EST: gi|211448816|gb|FL216203.1|FL216203
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|149078751|gb|EE167559.2|EE167559
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|14191238|gb|BG833468.1|BG833468
EST:     GGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|148936707|gb|EC880839.2|EC880839
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|149103813|gb|EE289222.2|EE289222
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|211273839|gb|FL423561.1|FL423561
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GTGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|148945420|gb|EC890649.2|EC890649
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|211169650|gb|FL398215.1|FL398215
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GTGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|148932562|gb|EC876390.2|EC876390
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|213191121|gb|FM184889.1|FM184889
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|71299529|gb|DR785773.1|DR785773
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|149094979|gb|EE180570.2|EE180570
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|31355792|gb|CD440149.1|CD440149
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|211448813|gb|FL216200.1|FL216200
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTANAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|211450938|gb|FL216219.1|FL216219
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|14191239|gb|BG833469.1|BG833469
EST:     ACCCTAG-AAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGCGTTGCCCCACCAG
genomic: ACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|211314995|gb|FL374737.1|FL374737
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|149108828|gb|EE292991.2|EE292991
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|14191240|gb|BG833470.1|BG833470
EST:     AGGACGAGCAAACCCTAGAAAGCTACG                         GCGTCTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCA
genomic: AGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGT-TGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCA
EST: gi|149102545|gb|EE287901.2|EE287901
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|148931592|gb|EC874698.2|EC874698
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
EST: gi|211448817|gb|FL216204.1|FL216204
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACG                         GCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAG

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: 110

AAGGAGGTCGTAGCCGGGAGCTGCGACGTGCCGGCGCCGCAGCAGCGTCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAGCTGCATCCAGTGCACCTGCTGCTGCCAGCTCCCTTGCTTCATCTACTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 242

AAGGAGGTCGTAGCCGGGAGCTGCGACGTGCCGGCGCCGCAGCAGCGTCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAGCTGCATCCAGTGCACCTGCTGCTGCCAGCTCCCTTGCTTCATCTACTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 265

AAGGAGGTCGTAGCCGGGAGCTGCGACGTGCCGGCGCCGCAGCAGCGTCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAGCTGCATCCAGTGCACCTGCTGCTGCCAGCTCCCTTGCTTCATCTACTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 139

AAGGAGGTCGTAGCCGGGAGCTGCGACGTGCCGGCGCCGCAGCAGCGTCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGAAAGCTACGgtacgtgcca ... tatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAGCTGCATCCAGTGCACCTGCTGCTGCCAGCTCCCTTGCTTCATCTACTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatttaatcctggaattgttaagaaattttagatacacatgcttatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAGCTGCATCCAGTGCACCTGCTGCTGCCAGCTCCCTTGCTTCATCTACTCT
   atttaat  putative branch site (score: 139)
               aattgttaagaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatcagatatatgaaccttctctttcttcctttgtctttgatttatgatttaatcctggaattgttaagaaattttagatacacatgcttatattgtagGCGTTGAGACAGATCACACAATTCACTTGGTGCGTGGTGTTGCCCCACCAGCTGCATCCAGTGCACCTGCTGCTGCCAGCTCCCTTGCTTCATCTACTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgct