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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACTACGCTGTCGTCCTCTGCAACTACGGCCCCGCCCTCCTCACCGGCGGCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcctcacgtagctagggagtggggtggggagattcggatgggtcgtccttccggagaaatatctgctcttttggtggtgaagatgctaacatc...

Basic information

species Zea mays
transcript GRMZM2G027307_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027307_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g58960.1 (Oryza sativa), 5'ss of exon 1
CTACTACGCTGTCGTCCTCTGCAACTACGGCCCCGCCCTCCTCACCGGCGGCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcctcacgtag-ctagggagtggggtggggagattcggatgggtcgtccttccggagaaatatctgctcttttggtggtgaagatgctaacatc--
||||||||| |||||  | | ||||||||||||||| ||| || ||||||||| || ||| |||  ||||||||  |||||||||||||||||||| |||||   ||    | || |  ||   | | |||| |||| | || || ||  ||         || ||  ||  |||  || ||| |  |    || |  |    
CTACTACGCGGTCGTGGTGTACAACTACGGCCCCGCGCTCTTCGCCGGCGGCGCCAGCACCCTCCTCGCGCTCGTCGTCCTGCTCCTCTTCCACTTCCTGgtaactattggctcgaactcttaaggggggggggggggggtttgggtg--tcaaaaacggtgaaaacgattagctggttgggtcg-aatctcgcaagtagacg
















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|148936501|gb|EC880614.2|EC880614
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTTCTGTGGTGCTCACTGACCCTGG
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTT-CTGTGGTGCTCACTGACCCTGG
EST: gi|148930766|gb|EC873088.2|EC873088
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|149065632|gb|EE286754.2|EE286754
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|91874476|gb|EB404433.1|EB404433
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|148939721|gb|EC884401.2|EC884401
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|148933153|gb|EC876792.2|EC876792
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|101393690|gb|EB818777.1|EB818777
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|76016944|gb|DT944114.1|DT944114
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|149072486|gb|EE160764.2|EE160764
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|149004888|gb|EE039399.2|EE039399
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|89762356|gb|DY689977.1|DY689977
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|91875637|gb|EB405594.1|EB405594
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|148956328|gb|EC902132.2|EC902132
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|148966764|gb|EE017849.2|EE017849
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|50326451|gb|CO521577.1|CO521577
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|60343523|gb|DN210496.1|DN210496
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|149110924|gb|EE294422.2|EE294422
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|148932453|gb|EC876177.2|EC876177
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
EST: gi|101399438|gb|EB821591.1|EB821591
EST:     GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGT

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: 99

CTACTACGCTGTCGTCCTCTGCAACTACGGCCCCGCCCTCCTCACCGGCGGCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGTTCTGTTCCACCAAATTGGAATCTTGATTTTGATGCGGAGAGGGGAGAAA


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

CTACTACGCTGTCGTCCTCTGCAACTACGGCCCCGCCCTCCTCACCGGCGGCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGTTCTGTTCCACCAAATTGGAATCTTGATTTTGATGCGGAGAGGGGAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

CTACTACGCTGTCGTCCTCTGCAACTACGGCCCCGCCCTCCTCACCGGCGGCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGTTCTGTTCCACCAAATTGGAATCTTGATTTTGATGCGGAGAGGGGAGAAA


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

CTACTACGCTGTCGTCCTCTGCAACTACGGCCCCGCCCTCCTCACCGGCGGCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTGGTGCTCACTGACCCTGGTTCTGTTCCACCAAATTGGAATCTTGATTTTGATGCGGAGAGGGGAGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACTACGCTGTCGTCCTCTGCAACTACGGCCCCGCCCTCCTCACCGGCGGCGGCACCACTCTCGCCGCGCTCGCTGTCCTGCTCCTCTTCCACTTTCTGgtgcgtagcctcacgtagctagggagtggggtggggagattcggatgggtcgtccttccggagaaatatctgctcttttggtggtgaagatgctaacatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaaata