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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGGCAGCGCCGTCCGGCGGTGGGGGCGGCGGTGCGGGGGAGGGCTCCTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacccctgctcctcctcctcctcatcgggctttcgtgtttagtctcggtgaagcgtttgtgctggagcgcagctaaccacggtcggattgggca...

Basic information

species Zea mays
transcript GRMZM2G100794_T01
intron # 1
splice site 5'
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|71439755|gb|DR820805.1|DR820805
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|149000507|gb|EE037687.2|EE037687
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|148938171|gb|EC882453.2|EC882453
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|211078940|gb|FL257763.1|FL257763
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|149083012|gb|EE172259.2|EE172259
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|71772125|gb|DR970062.1|DR970062
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|78089927|gb|DV518301.1|DV518301
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|148944209|gb|EC889301.2|EC889301
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|211078942|gb|FL257765.1|FL257765
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|211303560|gb|FL306497.1|FL306497
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|71765018|gb|DR962955.1|DR962955
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|148959485|gb|EC905484.2|EC905484
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|148946035|gb|EC891334.2|EC891334
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|71315475|gb|DR794342.1|DR794342
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|78086204|gb|DV514597.1|DV514597
EST:     CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: CTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
EST: gi|8367349|gb|BE050294.1|BE050294
EST:     GCAGGTATGACGATCGGGGCCCACGGGGTGGACCAAG                         TCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC
genomic: GCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGC

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: 78

GTGATGGCAGCGCCGTCCGGCGGTGGGGGCGGCGGTGCGGGGGAGGGCTCCTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGCCATACCCAGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGAC


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

GTGATGGCAGCGCCGTCCGGCGGTGGGGGCGGCGGTGCGGGGGAGGGCTCCTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGCCATACCCAGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

GTGATGGCAGCGCCGTCCGGCGGTGGGGGCGGCGGTGCGGGGGAGGGCTCCTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGCCATACCCAGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

GTGATGGCAGCGCCGTCCGGCGGTGGGGGCGGCGGTGCGGGGGAGGGCTCCTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacc ... tatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGCCATACCCAGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGGCAGCGCCGTCCGGCGGTGGGGGCGGCGGTGCGGGGGAGGGCTCCTCCTCGGCCGCCGCAGCTATGACGATCGGGGCCCACGGGGTGGACCAAGgttagcaacccctgctcctcctcctcctcatcgggctttcgtgtttagtctcggtgaagcgtttgtgctggagcgcagctaaccacggtcggattgggca

- - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcctcc