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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcagaccgatgcgcctctctttgttagattccaagtctgggcagagtgctttctaacagatgaatctctctcaaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTAAGGTGGGCAAATTGACAAATGATATCGTCGGAGAAGCCAGCCAGATGGG

Basic information

species Zea mays
transcript GRMZM2G369912_T01
intron # 3
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|33095312|gb|CF055306.1|CF055306
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTA
EST: gi|93016672|gb|EB642192.1|EB642192
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|211182071|gb|FL377604.1|FL377604
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GT---CGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|148965285|gb|EE016089.2|EE016089
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|166684656|gb|EG057120.1|EG057120
EST:     CGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: CGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|211133221|gb|FL428361.1|FL428361
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GT---CGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|22935402|gb|BU571677.1|BU571677
EST:     TCTCGACCCTTATCCCGGCAGTTTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACCTTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|87157382|gb|DY402171.1|DY402171
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|26457005|gb|CA828588.1|CA828588
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|20811198|gb|BQ295676.1|BQ295676
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|22935403|gb|BU571678.1|BU571678
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|213172910|gb|FM191134.1|FM191134
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCA--T-                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|26560104|gb|CA832339.1|CA832339
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
EST: gi|78544946|gb|DV622444.1|DV622444
EST:     TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTG                         GTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA
genomic: TCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTA

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), 43 (downstream exon)
Score: 53

TTGAAGAGATGGCATCAGCGAAAGCGACAAGCGGCGCGGCAGTTCTCGTCTCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTAAGGTGGGCAAATTGACAAATGATATCGTCGGAGAAGCCAGCCAGATGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

TTGAAGAGATGGCATCAGCGAAAGCGACAAGCGGCGCGGCAGTTCTCGTCTCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTAAGGTGGGCAAATTGACAAATGATATCGTCGGAGAAGCCAGCCAGATGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 121

TTGAAGAGATGGCATCAGCGAAAGCGACAAGCGGCGCGGCAGTTCTCGTCTCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTAAGGTGGGCAAATTGACAAATGATATCGTCGGAGAAGCCAGCCAGATGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

TTGAAGAGATGGCATCAGCGAAAGCGACAAGCGGCGCGGCAGTTCTCGTCTCTCGACCCTTATCCCGGCAGTCTTCGGCTGTGTAGCGAATTTTCATGTGgtaatcagac ... aaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTAAGGTGGGCAAATTGACAAATGATATCGTCGGAGAAGCCAGCCAGATGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccaagtctgggcagagtgctttctaacagatgaatctctctcaaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTAAGGTGGGCAAATTGACAAATGATATCGTCGGAGAAGCCAGCCAGATGGG
                       ttctaac  putative branch site (score: 99)
                                     tctctctca  putative PPT
                                             aaatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcagaccgatgcgcctctctttgttagattccaagtctgggcagagtgctttctaacagatgaatctctctcaaatttctagGTGGTCGTGAGAACATTGTACAGGATTGAGTTGTATATACGAGGTATATTAAGGTGGGCAAATTGACAAATGATATCGTCGGAGAAGCCAGCCAGATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG