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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggctcttctacgacaacacccttccacgccacgccctaaaaacaatagaatcttgtcgattagttcgctgagtttgatttttgctactgatgatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGT

Basic information

species Zea mays
transcript GRMZM5G823750_T02
intron # 2
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|211540347|gb|FL091515.1|FL091515
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211540346|gb|FL091514.1|FL091514
EST:     GAGGCGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|78116158|gb|DV534546.1|DV534546
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|78120227|gb|DV538611.1|DV538611
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211540349|gb|FL091517.1|FL091517
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|76013572|gb|DT940742.1|DT940742
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211131059|gb|FL391857.1|FL391857
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTC
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTC
EST: gi|29576943|gb|CB617055.1|CB617055
EST:     GTGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543360|gb|FL091529.1|FL091529
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGARACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543361|gb|FL091530.1|FL091530
EST:     GAGGCGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|101385030|gb|EB814560.1|EB814560
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|84980380|gb|DW530729.1|DW530729
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543355|gb|FL091524.1|FL091524
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543350|gb|FL091519.1|FL091519
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543352|gb|FL091521.1|FL091521
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211540348|gb|FL091516.1|FL091516
EST:     GAGGCGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543357|gb|FL091526.1|FL091526
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTT-GAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543362|gb|FL091531.1|FL091531
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCGTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543353|gb|FL091522.1|FL091522
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543349|gb|FL091518.1|FL091518
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|24462553|gb|BM660084.1|BM660084
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|76011928|gb|DT939098.1|DT939098
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|91050221|gb|EB160639.1|EB160639
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|78116574|gb|DV534961.1|DV534961
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543359|gb|FL091528.1|FL091528
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543351|gb|FL091520.1|FL091520
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|211543354|gb|FL091523.1|FL091523
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGARACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
EST: gi|33770746|gb|CF273040.1|CF273040
EST:     GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG                         GGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT
genomic: GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTT

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), 47 (downstream exon)
Score: 134

GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 96

GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 109

GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAGgtaggctctt ... gatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatcttgtcgattagttcgctgagtttgatttttgctactgatgatgatgaagGGAGGTTTGACCCCCAAGGAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGT
                                      tactgat  putative branch site (score: 109)
                          tttgattttt  TA-rich tract