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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTCTAGCGATGTTCTGCGCCTGAAGCAACTTGGTGTAAGAGGAGTTGTTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttcttttacctcttgtagctgcaggaattacttttatttctctctgaacttataatgttattacttgaccaagagaactataggatgtatcct...

Basic information

species Zea mays
transcript GRMZM2G031435_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031435_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g44910.1 (Oryza sativa), 5'ss of exon 2
GTTCTCTAGCGATGTTCTGCGCCTGAAGCAACTTGGTGTAAGAGGAGTTGTTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatg--ttcttttacct---cttgtagctgcaggaattacttttatttctctctgaacttataatgttattacttgaccaagagaactataggatgtatcct
 |||||||| ||||| | ||  || ||||||||||| ||||| || ||||| ||||| |||||| | ||||||||||||||||| |||||||||||||||||| ||   | | || ||||    ||||||||||||   ||  |   || | ||       || |      ||   || | | |  |   | | |  |  ||   
TTTCTCTAGTGATGTACCGCATCTCAAGCAACTTGGAGTAAGGGGCGTTGTCACACTGAATGAATCGTATGAAACTCTGGTTCCAACATCCTTATACCAGgtaaataaataccttcacctgattttgtagctgcagattttcttggcatgtatcaagatctttgtgcgtgcatatttttatctactg--ttcttgttttcat---
















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|88753204|gb|DY537345.1|DY537345
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAA
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAA
EST: gi|71441815|gb|DR822865.1|DR822865
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|148970664|gb|EE021375.2|EE021375
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTT
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTT
EST: gi|93284231|gb|EB676495.1|EB676495
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|71448351|gb|DR829401.1|DR829401
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|71439137|gb|DR820187.1|DR820187
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|211118445|gb|FL049561.1|FL049561
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCAACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTA
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTA
EST: gi|88746187|gb|DY530328.1|DY530328
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|71766612|gb|DR964549.1|DR964549
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|19057494|gb|BM736161.1|BM736161
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCAACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|78103952|gb|DV522370.1|DV522370
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|71430075|gb|DR811125.1|DR811125
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|76288945|gb|DV028513.1|DV028513
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|76280780|gb|DV020348.1|DV020348
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|87152319|gb|DY397108.1|DY397108
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCAACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|76928948|gb|DV171821.1|DV171821
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGT
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGT
EST: gi|74232090|gb|DT640004.1|DT640004
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|101383931|gb|EB814020.1|EB814020
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
EST: gi|22491044|gb|BU050967.1|BU050967
EST:     TTACACTCAATGAACCCTATGAAACTCTGGTTCCAACATCCTTATACCAG                         GCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC
genomic: TTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCC

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), 49 (downstream exon)
Score: 69

GTTCTCTAGCGATGTTCTGCGCCTGAAGCAACTTGGTGTAAGAGGAGTTGTTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCCCCATCCCTGGAGCATATTTGTCGTGCAGTGGATTTTATCCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

GTTCTCTAGCGATGTTCTGCGCCTGAAGCAACTTGGTGTAAGAGGAGTTGTTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCCCCATCCCTGGAGCATATTTGTCGTGCAGTGGATTTTATCCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

GTTCTCTAGCGATGTTCTGCGCCTGAAGCAACTTGGTGTAAGAGGAGTTGTTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCCCCATCCCTGGAGCATATTTGTCGTGCAGTGGATTTTATCCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

GTTCTCTAGCGATGTTCTGCGCCTGAAGCAACTTGGTGTAAGAGGAGTTGTTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttc ... tacttttcagGCTCATGGAATCAATCATCTCAAAATTCCTACAAGAGACTACCTGTTTGCCCCATCCCTGGAGCATATTTGTCGTGCAGTGGATTTTATCCATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTCTAGCGATGTTCTGCGCCTGAAGCAACTTGGTGTAAGAGGAGTTGTTACACTCAATGAACCCTATGAAACTCTGGTTCCGACATCCTTATACCAGgtagatgttcttttacctcttgtagctgcaggaattacttttatttctctctgaacttataatgttattacttgaccaagagaactataggatgtatcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagagaa