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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgaccaagatcttggagtcctaaaagatcagatcaatgattactatggagattgcatgtgtttttgtaccagtctaatgttattgtactatgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG

Basic information

species Zea mays
transcript GRMZM2G161566_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161566_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g51410.2 (Oryza sativa), 3'ss of exon 2
gtattgaccaagatcttggagtcctaaaagatcagatcaatgattactatggagattgcatgtgtttttgtaccagtctaatgttat-----tgtactatgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG
                    || ||  |  |||| ||||| |   ||  ||||| |||| ||| || ||  | || |||| |||| |     | |  | |  |||||||||||||||||||||||||| ||||| || || ||  ||||||||||| |||| |
--------------------gtactgcataatcaaatcaaaggcgacactggagtttgcttgttttcttccatcactcta-tgttctaaccatctgttttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTAGTTG
















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|89251386|gb|DY623172.1|DY623172
EST:     GTCATGAAAACTTGCATAAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAAAAGTTCTGTTCTACTTAAACGGGAGGGGTATTTACTTA
genomic: GTCATGAAAACTTGCATAA-CTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
EST: gi|211494300|gb|FL310097.1|FL310097
EST:     GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
EST: gi|211213913|gb|FL360058.1|FL360058
EST:     GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
EST: gi|211307749|gb|FL198216.1|FL198216
EST:     -TCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
EST: gi|211105937|gb|FL329403.1|FL329403
EST:     GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATT
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATT
EST: gi|211537841|gb|FL338654.1|FL338654
EST:     GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
EST: gi|211151343|gb|FL367847.1|FL367847
EST:     GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
EST: gi|211274785|gb|FL366576.1|FL366576
EST:     GTCATGAAAACTTGCATAACTCCGTTGACNAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
EST: gi|71447773|gb|DR828823.1|DR828823
EST:     GTCATGAAAATTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAGATCAGAAGAAGTTCTGAGCTACTTAAA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAA
EST: gi|211306681|gb|FL364492.1|FL364492
EST:     GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTYTANTTACTTA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
EST: gi|211424454|gb|FL316412.1|FL316412
EST:     GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG                         AGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA
genomic: GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTA

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: 47 (upstream exon), 48 (downstream exon)
Score: 73

GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 586

GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 645

GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG


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

GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGgtattgacca ... atgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggagattgcatgtgtttttgtaccagtctaatgttattgtactatgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG
                           gtctaat  putative branch site (score: 242)
                              taatgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgaccaagatcttggagtcctaaaagatcagatcaatgattactatggagattgcatgtgtttttgtaccagtctaatgttattgtactatgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT