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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgaatagtatatagctcacatatatgtatcatacatgcaggcagccttgtggtgtaacttgatctatgttttaccaacttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTCGTCAGGTTGTGAATGCTAGAAGATATGGAGCACTGCGAATTGCTCGGTT

Basic information

species Zea mays
transcript GRMZM2G058366_T01
intron # 14
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|12968301|gb|BG265247.1|BG265247
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|88746461|gb|DY530602.1|DY530602
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|148965008|gb|EE015841.2|EE015841
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|78118608|gb|DV536992.1|DV536992
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|211324539|gb|FL445891.1|FL445891
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAACGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|18163479|gb|BM333318.1|BM333318
EST:     TTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAGT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTT
genomic: TTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATA-Tgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTT
EST: gi|149062810|gb|EE157527.2|EE157527
EST:     TTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATTTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|5069977|gb|AI737942.1|AI737942
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAACGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|32865528|gb|CF005210.1|CF005210
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAACGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|5361078|gb|AI795693.1|AI795693
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|211198572|gb|FL471183.1|FL471183
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAACGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|12968903|gb|BG265744.1|BG265744
EST:     AAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: AAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|5005902|gb|AI711964.1|AI711964
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|60353761|gb|DN220734.1|DN220734
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|16921014|gb|BM074941.1|BM074941
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|211514505|gb|FL430894.1|FL430894
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAACGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|16916424|gb|BM072835.1|BM072835
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|211267809|gb|FL345566.1|FL345566
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAAGCAACAACGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|32941445|gb|CF046264.1|CF046264
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAACGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|149062811|gb|EE157528.2|EE157528
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|148965007|gb|EE015840.2|EE015840
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTTTCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|166539785|gb|EG136999.1|EG136999
EST:     AATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTAGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAACGTT
genomic: AATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCT-GATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTT
EST: gi|78021263|gb|DV489650.1|DV489650
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|86469050|gb|DY235420.1|DY235420
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
EST: gi|78118609|gb|DV536993.1|DV536993
EST:     TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATAT                         GTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC
genomic: TTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTC

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: 208

TCCCCTACTTTGAGACGTCGGCTAAAGAGGGCTTCAATGTAGAGGCTGCATTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTCGTCAGGTTGTGAATGCTAGAAGATATGGAGCACTGCGAATTGCTCGGTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 167

TCCCCTACTTTGAGACGTCGGCTAAAGAGGGCTTCAATGTAGAGGCTGCATTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTCGTCAGGTTGTGAATGCTAGAAGATATGGAGCACTGCGAATTGCTCGGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 199

TCCCCTACTTTGAGACGTCGGCTAAAGAGGGCTTCAATGTAGAGGCTGCATTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTCGTCAGGTTGTGAATGCTAGAAGATATGGAGCACTGCGAATTGCTCGGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 111

TCCCCTACTTTGAGACGTCGGCTAAAGAGGGCTTCAATGTAGAGGCTGCATTTGAGTGTATAGCGAGGAATGCTGTAAAAAATGAGCCAGAAGAAGATATgtaagtttga ... acttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTCGTCAGGTTGTGAATGCTAGAAGATATGGAGCACTGCGAATTGCTCGGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatgcaggcagccttgtggtgtaacttgatctatgttttaccaacttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTCGTCAGGTTGTGAATGCTAGAAGATATGGAGCACTGCGAATTGCTCGGTT
                                              cttttgc  CT-rich tract
                                 tatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgaatagtatatagctcacatatatgtatcatacatgcaggcagccttgtggtgtaacttgatctatgttttaccaacttttgcagGTATCTTCCTGATACGATTGATGTTGGGGGCGCTGGAAGGCAACAGCGTTCGTCAGGTTGTGAATGCTAGAAGATATGGAGCACTGCGAATTGCTCGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA