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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatcttagtgttttctgggatatgttaatatatttgattgggcggtagattgtcttccatgtagtttgtatctggtatcctcattgatttgtttccttttag

Basic information

species Zea mays
transcript GRMZM2G058498_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 4
GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatcttagtgttttctgggatatgttaatatatttgattgggcggtagattgtcttccatgtagtttgtatctggtatcctcattgatttgtttccttttag
||| |||||||||||||||||||||| |  ||||| |||||||| || || || ||||| ||||| ||||||||| | | |||      | |    | |  |  | || |  | |||  |||  || | |       |||| | || | ||||||||||||||| || | ||
GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctcaatatttctctcaagaccacatt-cacataat-gtacagta--ttgattttccta------gtatttagtgtgctcattgatttgttttctatcag
















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|37418983|gb|CF647165.1|CF647165
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211052947|gb|FL232812.1|FL232812
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|71319015|gb|DR796255.1|DR796255
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211049994|gb|FL232801.1|FL232801
EST:     GTTGGTGGTAACAG-CAAGCCAAAGGCGTCCATTTCTCATGGATCAGCCG                         GTTCTCTGCTCGGNTTGGAAGGATGATGGAACTACTGTCTT
genomic: GTTGGTGGTAACAGTCA-GCCAAAGGCGTCCATTTCTCATG-ATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTT
EST: gi|71435207|gb|DR816257.1|DR816257
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211049997|gb|FL232804.1|FL232804
EST:     TGTTGGTGGTAACAGTCAGCCAAAGS-GTNCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TGTTGGTGGTAACAGTCAGCCAAAGGCGT-CCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211052943|gb|FL232808.1|FL232808
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|67019316|gb|CO448065.1|CO448065
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211052951|gb|FL232816.1|FL232816
EST:     GTTGGTGGTARCAGTCAGCCGAAAGS-GTCCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGG
genomic: GTTGGTGGTAACAGTCAGCC-AAAGGCGTCC-ATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGG-
EST: gi|31355022|gb|CD439379.1|CD439379
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211050000|gb|FL232807.1|FL232807
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|32915973|gb|CF020785.1|CF020785
EST:     TTGTTGGTGGTAACAGTCAGTCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|71427496|gb|DR808546.1|DR808546
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211049999|gb|FL232806.1|FL232806
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211052950|gb|FL232815.1|FL232815
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGSSGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211052945|gb|FL232810.1|FL232810
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGS-GTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|78092605|gb|DV520979.1|DV520979
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211052946|gb|FL232811.1|FL232811
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATCGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211049992|gb|FL232799.1|FL232799
EST:     TGTTGGTGGTAACAGTCAGCCAAAGS-GTNCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TGTTGGTGGTAACAGTCAGCCAAAGGCGT-CCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|71765073|gb|DR963010.1|DR963010
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211049998|gb|FL232805.1|FL232805
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTYTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|32868065|gb|CF007747.1|CF007747
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|62550552|gb|DN830972.1|DN830972
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|71310174|gb|DR791376.1|DR791376
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211049995|gb|FL232802.1|FL232802
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211052953|gb|FL232818.1|FL232818
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|211052952|gb|FL232817.1|FL232817
EST:     TGTTGGTGGTAACAGTCAGCCAAAGGSGTCCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TGTTGGTGGTAACAGTCAGCCAAAGGCGTCC-ATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|50339684|gb|CO534810.1|CO534810
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|33102995|gb|CF062955.1|CF062955
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|32943595|gb|CF048414.1|CF048414
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
EST: gi|67024188|gb|CO452937.1|CO452937
EST:     TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG                         GTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC
genomic: TTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGC

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), 44 (downstream exon)
Score: 97

GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGCTGTGACAAGCAGGTCAAAATGTGGCCTCTTCTGTCAGGTGGGCAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGCTGTGACAAGCAGGTCAAAATGTGGCCTCTTCTGTCAGGTGGGCAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGCTGTGACAAGCAGGTCAAAATGTGGCCTCTTCTGTCAGGTGGGCAGCCTC


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

GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatctt ... ttccttttagGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGCTGTGACAAGCAGGTCAAAATGTGGCCTCTTCTGTCAGGTGGGCAGCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatcttagtgttttctgggatatgttaatatatttgattgggcggtagattgtcttccatgtagtttgtatctggtatcctcattgatttgtttccttttag

- - - - - - - - - - TGGTGG