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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcacttctaatgacctttcgtttgttaatccactcgggcccttattctgcccaccctgacgccaacaaaattgttgttcaattgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAGGAGGACCGGTTGCCTTGTGATGGCTAAGCTTTTTCCCCACTTGCTGACT

Basic information

species Zea mays
transcript GRMZM2G348675_T02
intron # 23
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|33096233|gb|CF056227.1|CF056227
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|60401356|gb|DN234163.1|DN234163
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|89106042|gb|DY576259.1|DY576259
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|33098458|gb|CF058418.1|CF058418
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGT
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGT
EST: gi|166530344|gb|EG051643.1|EG051643
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATA
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATA
EST: gi|116823199|gb|EC866720.1|EC866720
EST:     GGTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|31611836|gb|CD568458.1|CD568458
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|211241122|gb|FL071392.1|FL071392
EST:     GTTCAGCCGAGTCTGGAATGGTGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|60337110|gb|DN204083.1|DN204083
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|91056201|gb|EB166619.1|EB166619
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|37375043|gb|CF623932.1|CF623932
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|60394400|gb|DN227270.1|DN227270
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|8516300|gb|BE123026.1|BE123026
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|78077107|gb|DV505541.1|DV505541
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|21843367|gb|BQ703948.1|BQ703948
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|32938062|gb|CF042881.1|CF042881
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|6526938|gb|AW216185.1|AW216185
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|6012524|gb|AW061961.1|AW061961
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|60342258|gb|DN209231.1|DN209231
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|31406262|gb|CD484994.1|CD484994
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|60358719|gb|DN225692.1|DN225692
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|32910038|gb|CF014850.1|CF014850
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|8516418|gb|BE123144.1|BE123144
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTCCCATGGAGTTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|87157582|gb|DY402371.1|DY402371
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|33095636|gb|CF055630.1|CF055630
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|21432401|gb|BQ547891.1|BQ547891
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG
EST: gi|33095263|gb|CF055257.1|CF055257
EST:     GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATCTCATATGT
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGT
EST: gi|78024348|gb|DV492735.1|DV492735
EST:     GTTCAGCCGAGTTTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAG                         GAGTTCCTGATTTTCGAGAGGGAATATTTCATATGTACAATGGAGCTTGAG
genomic: GTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAG

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: 228

TGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAGGAGGACCGGTTGCCTTGTGATGGCTAAGCTTTTTCCCCACTTGCTGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

TGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAGGAGGACCGGTTGCCTTGTGATGGCTAAGCTTTTTCCCCACTTGCTGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

TGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAGGAGGACCGGTTGCCTTGTGATGGCTAAGCTTTTTCCCCACTTGCTGACT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 70

TGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttcta ... tgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAGGAGGACCGGTTGCCTTGTGATGGCTAAGCTTTTTCCCCACTTGCTGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccttattctgcccaccctgacgccaacaaaattgttgttcaattgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAGGAGGACCGGTTGCCTTGTGATGGCTAAGCTTTTTCCCCACTTGCTGACT
                ccctgac  putative branch site (score: 70)
                          aacaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacttctaatgacctttcgtttgttaatccactcgggcccttattctgcccaccctgacgccaacaaaattgttgttcaattgtttgtcagGAGTTCCTGATTTTCGAGAGGGAATATCTCATATGTACAATGGAGTTTGAGGAGGACCGGTTGCCTTGTGATGGCTAAGCTTTTTCCCCACTTGCTGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA