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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctagctcatcacacgctctgcaaccattgtgtgattccatccatctatctatctatccttaatgtctgactcatggtgattttacaatgatatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCGATGCTGGCGAAGCCCACCGCGTACATGGGGAAGGCCTTCAAAGCTGCTG

Basic information

species Zea mays
transcript GRMZM2G098039_T01
intron # 11
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|37383322|gb|CF628665.1|CF628665
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|211088578|gb|FL093437.1|FL093437
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|78074430|gb|DV502864.1|DV502864
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|26456111|gb|CA827694.1|CA827694
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|78544985|gb|DV622483.1|DV622483
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|22549093|gb|BU101294.1|BU101294
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACCCTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|20802569|gb|BQ293619.1|BQ293619
EST:     GAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: GAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|78544975|gb|DV622473.1|DV622473
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|20513077|gb|BQ280263.1|BQ280263
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|74233159|gb|DT641073.1|DT641073
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|20301353|gb|BQ164296.1|BQ164296
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCG
EST: gi|8516598|gb|BE123323.1|BE123323
EST:     TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAG                         ACACTGGAGAG
genomic: TAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAG

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: 44 (upstream exon), 49 (downstream exon)
Score: 110

GAAGCTGCTGGGGCTTAAGAACCAGAAGGACCAGCATTTCTCGGATCTGATAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCGATGCTGGCGAAGCCCACCGCGTACATGGGGAAGGCCTTCAAAGCTGCTG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 151

GAAGCTGCTGGGGCTTAAGAACCAGAAGGACCAGCATTTCTCGGATCTGATAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCGATGCTGGCGAAGCCCACCGCGTACATGGGGAAGGCCTTCAAAGCTGCTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 411

GAAGCTGCTGGGGCTTAAGAACCAGAAGGACCAGCATTTCTCGGATCTGATAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCGATGCTGGCGAAGCCCACCGCGTACATGGGGAAGGCCTTCAAAGCTGCTG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 95

GAAGCTGCTGGGGCTTAAGAACCAGAAGGACCAGCATTTCTCGGATCTGATAGTGGAGCAGAAGGAGGAGCTGAAGAATCGCGCCAACCAGTTGATACAGgttagctagc ... atatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCGATGCTGGCGAAGCCCACCGCGTACATGGGGAAGGCCTTCAAAGCTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatctatctatccttaatgtctgactcatggtgattttacaatgatatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCGATGCTGGCGAAGCCCACCGCGTACATGGGGAAGGCCTTCAAAGCTGCTG
                   gtctgac  putative branch site (score: 95)
                                  attttacaatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagctagctcatcacacgctctgcaaccattgtgtgattccatccatctatctatctatccttaatgtctgactcatggtgattttacaatgatatgaacagACACTGGAGAGCTGTGGCTGGGAAGCTGCCATCGGTTGCGGTGGCATCTCGATGCTGGCGAAGCCCACCGCGTACATGGGGAAGGCCTTCAAAGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT