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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagagcctccatctctctctctctctctctgtttctttcttccccttcctgtccatccgtgagcagccgatgggtgggtgctcgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGGGGTGGTGGAGCGGGTCAACAAGCTGGTCTACGTCCGCACTCTTCGCGCG

Basic information

species Zea mays
transcript GRMZM2G150496_T01
intron # 1
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|148957413|gb|EC903470.2|EC903470
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|71442788|gb|DR823838.1|DR823838
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|71320540|gb|DR797014.1|DR797014
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|149072639|gb|EE160869.2|EE160869
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|149012762|gb|EE042651.2|EE042651
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|28361761|gb|CB240117.1|CB240117
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|71433918|gb|DR814968.1|DR814968
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|211356176|gb|FL303065.1|FL303065
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|71771798|gb|DR969735.1|DR969735
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|71442787|gb|DR823837.1|DR823837
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
EST: gi|149074916|gb|EE163369.2|EE163369
EST:     GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAA                         GGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG
genomic: GTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGG

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), 48 (downstream exon)
Score: 110

GCCTCGAGGCCGCGCTTCAAGAGCTCCAGTCCGTTGCGCCCGCCGCTGCCGTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGGGGTGGTGGAGCGGGTCAACAAGCTGGTCTACGTCCGCACTCTTCGCGCG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 57

GCCTCGAGGCCGCGCTTCAAGAGCTCCAGTCCGTTGCGCCCGCCGCTGCCGTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGGGGTGGTGGAGCGGGTCAACAAGCTGGTCTACGTCCGCACTCTTCGCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GCCTCGAGGCCGCGCTTCAAGAGCTCCAGTCCGTTGCGCCCGCCGCTGCCGTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGGGGTGGTGGAGCGGGTCAACAAGCTGGTCTACGTCCGCACTCTTCGCGCG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 37

GCCTCGAGGCCGCGCTTCAAGAGCTCCAGTCCGTTGCGCCCGCCGCTGCCGTCACCGTCGCGGACACCATTCCCGTCAATCAAGAGGACAACATCCTCAAgtacagagcc ... cgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGGGGTGGTGGAGCGGGTCAACAAGCTGGTCTACGTCCGCACTCTTCGCGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagagcctccatctctctctctctctctctgtttctttcttccccttcctgtccatccgtgagcagccgatgggtgggtgctcgtggcgcagGGGGCATGGGACGTCGGACCAGGACGGGGAGGTGGTTGCGACGCTCTGCGGGGTGGTGGAGCGGGTCAACAAGCTGGTCTACGTCCGCACTCTTCGCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG