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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggtttgttaactagagattctttttctttggcatccgactcaggagttccaacgcactacttgtttcgttaacatcacacttgctttttccttgcttcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAGACACTTTTTTGTCGAGCATCTGTTCGATGATCTGCATCAAGGTCAACCA

Basic information

species Zea mays
transcript GRMZM5G823750_T02
intron # 5
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|5791479|gb|AI978271.1|AI978271
EST:     AGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGATTGAAGTTGTGAGAAG
genomic: AGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|78116158|gb|DV534546.1|DV534546
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|78120227|gb|DV538611.1|DV538611
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|211540349|gb|FL091517.1|FL091517
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAAGT-GTGAGAA
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAA-GTTGTGAGAA
EST: gi|60395120|gb|DN227989.1|DN227989
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGATTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|76013572|gb|DT940742.1|DT940742
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|29576943|gb|CB617055.1|CB617055
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|6022643|gb|AW067455.1|AW067455
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGATTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|101385030|gb|EB814560.1|EB814560
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|84980380|gb|DW530729.1|DW530729
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|211543350|gb|FL091519.1|FL091519
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTG
EST: gi|211540348|gb|FL091516.1|FL091516
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGG
EST: gi|78116157|gb|DV534545.1|DV534545
EST:     GCTTTTAGACAGGAAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: GCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|211543362|gb|FL091531.1|FL091531
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|6056596|gb|AW091001.1|AW091001
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGATTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|76011928|gb|DT939098.1|DT939098
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|60351828|gb|DN218801.1|DN218801
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|91050221|gb|EB160639.1|EB160639
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|78116574|gb|DV534961.1|DV534961
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|6194514|gb|AW146618.1|AW146618
EST:     TTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGATTGAAGTTGTGAGAAG
genomic: TTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|29544924|gb|CB605532.1|CB605532
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
EST: gi|33770746|gb|CF273040.1|CF273040
EST:     CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAAT                         AATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG
genomic: CTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAG

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: 117

TTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAGACACTTTTTTGTCGAGCATCTGTTCGATGATCTGCATCAAGGTCAACCA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 110

TTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAGACACTTTTTTGTCGAGCATCTGTTCGATGATCTGCATCAAGGTCAACCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 88

TTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAGACACTTTTTTGTCGAGCATCTGTTCGATGATCTGCATCAAGGTCAACCA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 126

TTATTGTCGGAAAGGCCTGTGCTAATGAAACCTGGCATCAATTGCCTGAACTGCTTTTAGACAGGGAAGAAGGACGCATGAAGACAGAGCTAGCTAAAATgtgcggtttg ... tcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAGACACTTTTTTGTCGAGCATCTGTTCGATGATCTGCATCAAGGTCAACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgcactacttgtttcgttaacatcacacttgctttttccttgcttcattaacagAATACTCAATAAGCATAGTGATGACATATACCTGGTTGAAGTTGTGAGAAGACACTTTTTTGTCGAGCATCTGTTCGATGATCTGCATCAAGGTCAACCA
               cgttaac  putative branch site (score: 126)
                            cttgctttttccttgc  putative PPT
                                            ttcattaa  TA-rich tract