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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttattgcattgctgtgccccaagctccgccactgatactatgacttatgaaatggtttttatcttcattttagctcatgacactaatgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGGGCAGCATTGGGCTACTATCAGAGAAACCAAATAATCCCATACCTAACTG

Basic information

species Zea mays
transcript GRMZM2G160237_T02
intron # 4
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|78022261|gb|DV490648.1|DV490648
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTCTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|166607207|gb|EG111524.1|EG111524
EST:     GTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTCTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: GTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|108823835|gb|EC277843.1|EC277843
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTCTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|76280337|gb|DV019905.1|DV019905
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTTTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|166524217|gb|EG098999.1|EG098999
EST:     AATGTGATAGTGAAAGACCATTTTGCTTCCAGCAGCTCTAGCCTCTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAG
genomic: AATGTGATAGTGAAAG-CCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAG
EST: gi|60355946|gb|DN222919.1|DN222919
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|78080468|gb|DV508880.1|DV508880
EST:     GTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: GTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|78080469|gb|DV508881.1|DV508881
EST:     GTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: GTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|5325245|gb|AI783436.1|AI783436
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTCTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|60395923|gb|DN228793.1|DN228793
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCCTGGCGCCAAGTTTTGA
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGC-TGGCGCCAAGTTT-GA
EST: gi|166664749|gb|EG136529.1|EG136529
EST:     ATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTCTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTG
genomic: ATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTG
EST: gi|78115397|gb|DV533785.1|DV533785
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|31362821|gb|CD447178.1|CD447178
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|32855356|gb|CD995037.1|CD995037
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|60352028|gb|DN219001.1|DN219001
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|31353876|gb|CD438233.1|CD438233
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|5915483|gb|AW053124.1|AW053124
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTCTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|14243601|gb|BG841261.2|BG841261
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|213183032|gb|FM189492.1|FM189492
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|32834193|gb|CD973871.1|CD973871
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|14243907|gb|BG841579.2|BG841579
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
EST: gi|7145416|gb|AW506897.1|AW506897
EST:     AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAG                         GTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG
genomic: AAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGG

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: 248

CCAAATTCTGAAACCTGCTGAGAGAAAAAACAAATTTATGGGGTCCAACAAAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGGGCAGCATTGGGCTACTATCAGAGAAACCAAATAATCCCATACCTAACTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 204

CCAAATTCTGAAACCTGCTGAGAGAAAAAACAAATTTATGGGGTCCAACAAAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGGGCAGCATTGGGCTACTATCAGAGAAACCAAATAATCCCATACCTAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

CCAAATTCTGAAACCTGCTGAGAGAAAAAACAAATTTATGGGGTCCAACAAAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGGGCAGCATTGGGCTACTATCAGAGAAACCAAATAATCCCATACCTAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

CCAAATTCTGAAACCTGCTGAGAGAAAAAACAAATTTATGGGGTCCAACAAAATGTGATAGTGAAAGCCATTTTGCTTCCAGCAGCTCTAGCCTGTTAAGgtcagttaat ... tgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGGGCAGCATTGGGCTACTATCAGAGAAACCAAATAATCCCATACCTAACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttatgaaatggtttttatcttcattttagctcatgacactaatgttgtgtagGTTCTCCTGTGGATGCATCGAGACAACAGCATGCTGGCGCCAAGTTTGAGGGCAGCATTGGGCTACTATCAGAGAAACCAAATAATCCCATACCTAACTG
                                       cactaat  putative branch site (score: 247)
              tttttatcttcatttt  TA-rich tract