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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactgcttcttgtcacctttgaatgctgccttttctgcctatacaattatataaggagtaatccatgccattccaacttctgtttcttctactcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 12
----------------------------------cactgcttcttgtcacctttgaatgctgccttttctgcctatacaattatataaggagtaatccatgc--cattccaacttctgtttcttcta---------------------ctcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC
                                   |  | |  | ||||| |    |     |  |   |  ||| |||| | ||| |  ||||||  ||||  | ||    | | ||||  |||||                     ||  |||||||||| ||||| ||||| || |||||||| ||||| | ||| || || ||||| ||| |||||||||||||||| |||| ||||||||| || || ||||
gtatgttttatattttatttttgtctgtattgtgtataggtcatggtcacatacacacatcacactaa-tatcta-acaagtgtatga--agtaatttatgcttcctttatgcctatgttctttctaaatggctaatccttgccatcccttctgcagATACGTTTTGCTAGTGTGGACATGGAGCTGCATACGACTTACGATCCAAATGGTTCATTGTCCATATATGATGTCGACCGAAGAGTTGCTGAGCGAACAC
















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|14243309|gb|BG841007.2|BG841007
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|5871243|gb|AW017714.1|AW017714
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|211206211|gb|FL245890.1|FL245890
EST:     AGCTTGKAGCTGCAAARAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|6020894|gb|AW065822.1|AW065822
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|60401020|gb|DN233827.1|DN233827
EST:     CTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: CTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|20507576|gb|BQ279691.1|BQ279691
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGT
EST: gi|14242856|gb|BG840631.2|BG840631
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|31997605|gb|CD661676.1|CD661676
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|31664241|gb|CD572966.1|CD572966
EST:     AGCTTGTAGCTGCAAAGAATTTCCGNGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCA
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCA
EST: gi|40336438|gb|CK370508.1|CK370508
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|149075397|gb|EE163911.2|EE163911
EST:     TTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: TTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|28982897|gb|BQ538418.2|BQ538418
EST:     GCTTGTAGCTGCAAAAGAATTTCCGTGCTGGCACCTTGAGCNTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: GCTTGTAGCTGC-AAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|29543522|gb|CB603904.1|CB603904
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|149009255|gb|EE153869.2|EE153869
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|26456915|gb|CA828498.1|CA828498
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|67025999|gb|CO454748.1|CO454748
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|15589996|gb|BI674612.1|BI674612
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|71758760|gb|DR956697.1|DR956697
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
EST: gi|110220920|gb|EC902818.1|EC902818
EST:     AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAG                         ATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT
genomic: AGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAAT

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: 238

TGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

TGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

TGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

TGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGCACCTTGAGCCTGCGTCAGgtccgtaagc ... actcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatataaggagtaatccatgccattccaacttctgtttcttctactcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC
                               cttctgtttcttctac  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactgcttcttgtcacctttgaatgctgccttttctgcctatacaattatataaggagtaatccatgccattccaacttctgtttcttctactcgtgcagATACGATTTGCCAGTGTAGATATGGAGCTTCATACAAGTTATGACCCCAATGGCTCAGTGTCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACAC

- ctgcttc
- - - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - - ttctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcca