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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatttatgttctgcagtgttataggctcttatttagtttaagtacagtagcactaatagtaattaatacgacttaatatcgatcataactctaatgtcatcattcttgaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA

Basic information

species Zea mays
transcript GRMZM2G073950_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 3'ss of exon 5
gtaagttatttatgttctgcagtgttataggctcttatttagtttaagtacagtagcactaatagtaattaatacgacttaatatcgatcataactctaatgtcatcattcttgaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA
|||||||||||||||| | ||||| |||      ||  ||  |  |||  ||  ||||    |||||| |||| | |  | |  | ||  ||  || | ||  |   |   ||  ||| |||||||| || |||||||||||||| |||||||||||||| || ||||  |||| ||||||||||||  |||| ||||| ||||||||||| || || |||||
gtaagttatttatgttgttcagtgatattaatgtttggttc-tgaaagagcatgagcag-ggtagtaactaatgcaatatcacct-gactat--cttttatcgctaaaccattatcctggtagGAATTTGTTGGGATCAGTGGTTCCCAGAGTGTGCAAGGGCCATGGTGCTTCAGGGGGCTGAAATTTTGTTCTATCCAACTGCAATTGGTTCTGAGCCCCA

upper sequence: GRMZM2G073950_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttatttatgttctgcagtgttataggctcttatttagtttaagtacagtagcactaatagtaattaatacgacttaatatcgatcataactctaatgtcatcattcttgaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA
                                  | |  |  | || | | |       |  || |      | ||   | |  || ||| ||| |    |   |      |  |   | |||  || || ||||||||||||||||| |||   ||  |||| ||||  || | ||| |||||||||||||||||||||||||| ||||| || ||||| ||
---------------------------------gtaagatgctctatgcagaactctgtttctaatgtccttttcgttgttacttc-atcttaattgatgtactaatgaaatgtattgtttagCTATATGTTGGGATCAGTGGTTTCCTGAGGCAGCTCGAGCTATGGTTCTACAGGGTGCTGAAATACTGTTTTATCCCACTGCTATTGGTTCTGAACCTCA
















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|211141687|gb|FL053515.1|FL053515
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|78077685|gb|DV506119.1|DV506119
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|211141683|gb|FL053511.1|FL053511
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|113702021|gb|EE679525.1|EE679525
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|32789123|gb|CD941359.1|CD941359
EST:     TAAGGCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: TAAGGCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|29130437|gb|CB381141.1|CB381141
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|101394654|gb|EB819259.1|EB819259
EST:     TTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: TTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|91056600|gb|EB167018.1|EB167018
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|148953399|gb|EE152896.2|EE152896
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|78081735|gb|DV510147.1|DV510147
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|88758160|gb|DY542301.1|DY542301
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|50324199|gb|CO519325.1|CO519325
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|84908437|gb|DW404315.1|DW404315
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|60346678|gb|DN213651.1|DN213651
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|148939361|gb|EC883888.2|EC883888
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|78078908|gb|DV507320.1|DV507320
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|71417126|gb|DR803932.1|DR803932
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|71417127|gb|DR803933.1|DR803933
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|29544724|gb|CB605104.1|CB605104
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|94478259|gb|EB707217.1|EB707217
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
EST: gi|78077686|gb|DV506120.1|DV506120
EST:     GCTTTCAAAACCAAGTATGCCACCATTGGTGTTG                         GAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC
genomic: GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTC

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: 34 (upstream exon), 49 (downstream exon)
Score: 153

GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 244

GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 270

GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 241

GCTTTCAAAACCAAGTATGCCACCATTGGTGTTGgtaagttatt ... gaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatacgacttaatatcgatcataactctaatgtcatcattcttgaccttgtagGAATCTGCTGGGATCAGTGGTTTCCAGAGTGTGCAAGAGCAATGGCACTTCTGGGGGCTGAAATACTGTTTTATCCCACTGCAATTGGATCCGAACCCCA
        acttaatat  TA-rich tract