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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgtcgtataaacaaaccgcaaaactgtcatttttaaatttttcttgcagacaatagctattggtaccaaatgcatgcttacgaaattctgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG

Basic information

species Zea mays
transcript GRMZM5G823750_T02
intron # 3
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:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211540346|gb|FL091514.1|FL091514
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|78116158|gb|DV534546.1|DV534546
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|78120227|gb|DV538611.1|DV538611
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211540349|gb|FL091517.1|FL091517
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|76013572|gb|DT940742.1|DT940742
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|29576943|gb|CB617055.1|CB617055
EST:     GTGGGTTCAGTACTGGGCACTTTTC-TTTTGTTGTTGGGTTCTCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: GTGGGTTCAGTACTGGGCAC-TTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543360|gb|FL091529.1|FL091529
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543361|gb|FL091530.1|FL091530
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|101385030|gb|EB814560.1|EB814560
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|84980380|gb|DW530729.1|DW530729
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTA
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543355|gb|FL091524.1|FL091524
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCAACTAATTCTCTATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543350|gb|FL091519.1|FL091519
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCAACTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543352|gb|FL091521.1|FL091521
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCAACTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211540348|gb|FL091516.1|FL091516
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543357|gb|FL091526.1|FL091526
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543362|gb|FL091531.1|FL091531
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|6056596|gb|AW091001.1|AW091001
EST:     CGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543353|gb|FL091522.1|FL091522
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543349|gb|FL091518.1|FL091518
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|24462553|gb|BM660084.1|BM660084
EST:     GTGGGTTCAGTACTGGGCACTTTCGCGATGTTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTTCACCTTATTCTCCATTAAGATTTTTTGACT
genomic: GTGGGTTCAGTACTGGGCACTTTCGCGATGTT-GTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTT-GACT
EST: gi|76011928|gb|DT939098.1|DT939098
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|60351828|gb|DN218801.1|DN218801
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|91050221|gb|EB160639.1|EB160639
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|78116574|gb|DV534961.1|DV534961
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTCGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543359|gb|FL091528.1|FL091528
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543351|gb|FL091520.1|FL091520
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCAACTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|211543354|gb|FL091523.1|FL091523
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
EST: gi|33770746|gb|CF273040.1|CF273040
EST:     CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAG                         GACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG
genomic: CGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTG

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: 25 (upstream exon), 36 (downstream exon)
Score: 12

GAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 29

GAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 15

GAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 26

GAGGAGGAGACGCTCCTGGCTTGCAATTTACTTCCTGGTGTTTATTTCATCGTGGGTTCAGTACTGGGCACTTTCGCGATGTTGTTGGGTTCCCACAAAGgttgctcact ... tgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcagacaatagctattggtaccaaatgcatgcttacgaaattctgttgtgcagGACTCAAATTGCTTGGGCGTCCACCTAATTCTCCATTAAGATCTTTGACTGTTTATG
                               tgcttac  putative branch site (score: 26)
                                          ttctgtt  putative PPT
                                       aaattct  TA-rich tract