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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagacacggttcatattattcagccgtggttcctctttcttatacaggatataggaaatacgcgacgtttcatttttttttctaatcgatttccggtccggcggtccctgtttttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGCTATGTGGACATGTCCACTGTTGACGCTGCAACTTCGACCAAGATTAGCG

Basic information

species Zea mays
transcript GRMZM2G153984_T01
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|60350258|gb|DN217231.1|DN217231
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|74244863|gb|DT652777.1|DT652777
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|71328008|gb|DR800651.1|DR800651
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|148969030|gb|EE019740.2|EE019740
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|148969718|gb|EE020590.2|EE020590
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|78084019|gb|DV512412.1|DV512412
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|101382897|gb|EB813502.1|EB813502
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|78119858|gb|DV538242.1|DV538242
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|211111950|gb|FL269638.1|FL269638
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|28931022|gb|CB334383.1|CB334383
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|71439692|gb|DR820742.1|DR820742
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|89764409|gb|DY691230.1|DY691230
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|50326300|gb|CO521426.1|CO521426
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|149051791|gb|EE155917.2|EE155917
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|50334992|gb|CO530118.1|CO530118
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|71448020|gb|DR829070.1|DR829070
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|149075802|gb|EE164336.2|EE164336
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|20512919|gb|BQ280105.1|BQ280105
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGTAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|28873957|gb|CB329877.1|CB329877
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|149081805|gb|EE170963.2|EE170963
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|148954590|gb|EC900032.2|EC900032
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|149079137|gb|EE168066.2|EE168066
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|89762144|gb|DY689877.1|DY689877
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|211111947|gb|FL269635.1|FL269635
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGANCCCAGCGCCGCCCTATCA                         GTCGTCTTCGA
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGA
EST: gi|211111949|gb|FL269637.1|FL269637
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|22133534|gb|BQ833766.1|BQ833766
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|76917425|gb|DV166840.1|DV166840
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|93013137|gb|EB638657.1|EB638657
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|149112755|gb|EE295578.2|EE295578
EST:     GTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTAATC-                         GTCGTCTTCCACAAGGATGGC
genomic: GTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTA-TCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGC
EST: gi|149073536|gb|EE161839.2|EE161839
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|22819821|gb|BU499911.1|BU499911
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|148967444|gb|EE018674.2|EE018674
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|20811286|gb|BQ295764.1|BQ295764
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
EST: gi|211111945|gb|FL269633.1|FL269633
EST:     AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCA                         GTCATCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC
genomic: AGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGC

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: 47 (upstream exon), 49 (downstream exon)
Score: 166

CGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGCTATGTGGACATGTCCACTGTTGACGCTGCAACTTCGACCAAGATTAGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 134

CGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGCTATGTGGACATGTCCACTGTTGACGCTGCAACTTCGACCAAGATTAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

CGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGCTATGTGGACATGTCCACTGTTGACGCTGCAACTTCGACCAAGATTAGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

CGCCGCGCTCGGCGCCACCGTCGGGGAGACGCCTGCCTCCGTCGTCTCCAAGTGCAGATACACCATCGCCATGCTCTCCGACCCCAGCGCCGCCCTATCAgttaagacac ... ttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGCTATGTGGACATGTCCACTGTTGACGCTGCAACTTCGACCAAGATTAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttttttttctaatcgatttccggtccggcggtccctgtttttccacctagGTCGTCTTCGACAAGGATGGCGTGCTCGAGCAGATCGGTAGCGGGAAGGGCTATGTGGACATGTCCACTGTTGACGCTGCAACTTCGACCAAGATTAGCG
           ttctaat  putative branch site (score: 101)
                                    tccctgtttttccacc  putative PPT
     ttttttttctaat  TA-rich tract