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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggcgaaacactgctagtactgttctttcgcttccattcaatcttactgctgagaagctcgatttgtgcaatggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGACACACGATTCTCTACGCTTCCCAGCCATCTGGTTATCTACTGGAGAACCC

Basic information

species Zea mays
transcript GRMZM2G017941_T01
intron # 7
splice site 3'
intron type U2

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|78025308|gb|DV493695.1|DV493695
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|71329488|gb|DR801466.1|DR801466
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|211169629|gb|FL169502.1|FL169502
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|60401365|gb|DN234172.1|DN234172
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|7242261|gb|AW574447.1|AW574447
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCGCGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|110524419|gb|EE028603.1|EE028603
EST:     TTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: TTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|16379938|gb|BI993223.1|BI993223
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|37383723|gb|CF628888.1|CF628888
EST:     GCGGCGGGTTCGAGAAG-TANGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: GCGGCGGGTTCGAGAAGTTA-GGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|31358873|gb|CD443230.1|CD443230
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|93281025|gb|EB673289.1|EB673289
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|13515990|gb|BG518266.1|BG518266
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCCCCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGCCTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|71329487|gb|DR801465.1|DR801465
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|37379701|gb|CF626599.1|CF626599
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|4834965|gb|AI670191.1|AI670191
EST:     TTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: TTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|78106618|gb|DV525036.1|DV525036
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|101399852|gb|EB821772.1|EB821772
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|211172988|gb|FL169531.1|FL169531
EST:     GTCTTCTGCAGCGGCGGGTTCGAGAAAGT-AGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTTCCCAGCT-GTCGACCTGCTGAAGCTGTCTGGGGCTAGA
genomic: GTCTTCTGCAGCGGCGGGTTCGAGAA-GTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTT-CCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGA
EST: gi|149013783|gb|EE043247.2|EE043247
EST:     CGTCTTCTGCAGCGGCGGGTTGGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|211172990|gb|FL169533.1|FL169533
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|67024634|gb|CO453383.1|CO453383
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|78106617|gb|DV525035.1|DV525035
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|4730421|gb|AI649587.1|AI649587
EST:     GGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: GGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
EST: gi|148982778|gb|EE028604.2|EE028604
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGT
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGT
EST: gi|37397410|gb|CF636002.1|CF636002
EST:     CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG                         GGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC
genomic: CGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGAC

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: 46 (upstream exon), 49 (downstream exon)
Score: 157

GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGACACACGATTCTCTACGCTTCCCAGCCATCTGGTTATCTACTGGAGAACCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 312

GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGACACACGATTCTCTACGCTTCCCAGCCATCTGGTTATCTACTGGAGAACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGACACACGATTCTCTACGCTTCCCAGCCATCTGGTTATCTACTGGAGAACCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 346

GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAGgttaggcgaa ... ggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGACACACGATTCTCTACGCTTCCCAGCCATCTGGTTATCTACTGGAGAACCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcttccattcaatcttactgctgagaagctcgatttgtgcaatggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGACACACGATTCTCTACGCTTCCCAGCCATCTGGTTATCTACTGGAGAACCC
             atcttac  putative branch site (score: 346)
        attcaat  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggcgaaacactgctagtactgttctttcgcttccattcaatcttactgctgagaagctcgatttgtgcaatggcaccacagGGGAGCTGCTTTCCCAGCTTGTCGACTTGCTGAAGCTGTCTGGGGCTAGACACACGATTCTCTACGCTTCCCAGCCATCTGGTTATCTACTGGAGAACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA