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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtacattttttcgtgaaacaaaagatcattttcattttaagccatttctgcaccaatatatattttttcctgatagtgatgcctttcttaccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG

Basic information

species Zea mays
transcript GRMZM2G129554_T02
intron # 12
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|32863381|gb|CF003063.1|CF003063
EST:     CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAA                         ATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG
genomic: CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG
EST: gi|26557921|gb|CA830156.1|CA830156
EST:     AGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCCTCAATTCTGAGAA                         ATTGAAGTCTCATTTTGAAGAGA
genomic: AGGAAGCGCGTCGACAAGACATAAAGAATGAAATCC-TCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGA
EST: gi|6102016|gb|AW126486.1|AW126486
EST:     CTGGAAGCGCGTCGACCAGACATAAAGAAAGAAATCCTCAATTCTGAGAA                         ATTGAAGTCTCATTTTGAAGAGAAT
genomic: CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAAT
EST: gi|21809935|gb|BQ668253.1|BQ668253
EST:     CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAA                         ATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTGATTT
genomic: CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTGATTT
EST: gi|87155790|gb|DY400579.1|DY400579
EST:     CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAA                         ATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG
genomic: CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG
EST: gi|26560161|gb|CA832396.1|CA832396
EST:     CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAA                         ATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG
genomic: CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG
EST: gi|32930851|gb|CF035663.1|CF035663
EST:     CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAA                         ATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG
genomic: CAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG

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: 47 (upstream exon), 48 (downstream exon)
Score: 132

GATGTTGCAAGGAGTGTGACAACACGTGATGTACAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 84

GATGTTGCAAGGAGTGTGACAACACGTGATGTACAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 65

GATGTTGCAAGGAGTGTGACAACACGTGATGTACAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 97

GATGTTGCAAGGAGTGTGACAACACGTGATGTACAGGAAGCGCGTCGACAAGACATAAAGAATGAAATCCTCAATTCTGAGAAgtaagatcct ... taccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctgcaccaatatatattttttcctgatagtgatgcctttcttaccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG
                                         ttcttac  putative branch site (score: 97)
                                    tgcctttcttacctt  CT-rich tract
           aatatatattttttcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtacattttttcgtgaaacaaaagatcattttcattttaagccatttctgcaccaatatatattttttcctgatagtgatgcctttcttaccttgtagATTGAAGTCTCATTTTGAAGAGAATCCAACGGACCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA