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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattatgagttgacttttgcagttgcacccaggaataattttgtaaatataactctagaaactattggttgtactaaagcaactttctatgctcaaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACCGTCACCGGAATCATTGAGGTTGTTGACAACACTACACTGAGGATCACTG

Basic information

species Zea mays
transcript GRMZM2G021270_T01
intron # 13
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|211094720|gb|FL034692.1|FL034692
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGCCAATACCGAAGG
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATAC-GAAGG
EST: gi|211094717|gb|FL034689.1|FL034689
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
EST: gi|211094713|gb|FL034685.1|FL034685
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
EST: gi|211097187|gb|FL034699.1|FL034699
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGTCAATAC-A-GGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
EST: gi|86465874|gb|DY232247.1|DY232247
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAGG                         GGGTCTATAGAAAAAACAGTCAATACAAAGGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
EST: gi|211094718|gb|FL034690.1|FL034690
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
EST: gi|211094721|gb|FL034693.1|FL034693
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
EST: gi|9794356|gb|BE552664.1|BE552664
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
EST: gi|211097189|gb|FL034701.1|FL034701
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
EST: gi|211094725|gb|FL034697.1|FL034697
EST:     TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAG                         GGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC
genomic: TGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACC

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: 336

TATTCCAAACTACAATCCAAGAGACATTGTTGCTAACGTCAGGCGGTTGTTGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACCGTCACCGGAATCATTGAGGTTGTTGACAACACTACACTGAGGATCACTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 33

TATTCCAAACTACAATCCAAGAGACATTGTTGCTAACGTCAGGCGGTTGTTGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACCGTCACCGGAATCATTGAGGTTGTTGACAACACTACACTGAGGATCACTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 27

TATTCCAAACTACAATCCAAGAGACATTGTTGCTAACGTCAGGCGGTTGTTGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACCGTCACCGGAATCATTGAGGTTGTTGACAACACTACACTGAGGATCACTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 38

TATTCCAAACTACAATCCAAGAGACATTGTTGCTAACGTCAGGCGGTTGTTGAATGAAGAGTCTACTGTACCAATGCATCCTTGGTATAGGGGATTCAAGgttagtatta ... caaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACCGTCACCGGAATCATTGAGGTTGTTGACAACACTACACTGAGGATCACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataactctagaaactattggttgtactaaagcaactttctatgctcaaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACCGTCACCGGAATCATTGAGGTTGTTGACAACACTACACTGAGGATCACTG
                       tactaaa  putative branch site (score: 38)
          aaactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtattatgagttgacttttgcagttgcacccaggaataattttgtaaatataactctagaaactattggttgtactaaagcaactttctatgctcaaattgcagGGGTCTATAGAGAAGACAGTCAATACGAAGGTAGCTGGTTCCACGTATACCGTCACCGGAATCATTGAGGTTGTTGACAACACTACACTGAGGATCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT