Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCGCCTCCTCTGGCGTCGCGTCCTGCTCCCTGCGCGCCGGCGGCGACTCCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttttcgtcttccccgtccctcctacctccccttgccattccattacttggtagcttcgaatcgggaggtacttgtctttgtttcgttatctgt...

Basic information

species Zea mays
transcript GRMZM2G042080_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|211285362|gb|FL347798.1|FL347798
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|76932372|gb|DV173030.1|DV173030
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|211287064|gb|FL337506.1|FL337506
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|101383237|gb|EB813674.1|EB813674
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGCGAAGGGGAACGAGG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGG-GA-GGGGA-CGAGG
EST: gi|211517502|gb|FL351631.1|FL351631
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|76287059|gb|DV026627.1|DV026627
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATACTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|211260647|gb|FL352281.1|FL352281
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|71421895|gb|DR805584.1|DR805584
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|148959395|gb|EC905430.2|EC905430
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|37426350|gb|CF650926.1|CF650926
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|89252849|gb|DY624635.1|DY624635
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|33467070|gb|CF244119.1|CF244119
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|148935525|gb|EC879566.2|EC879566
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|149075255|gb|EE163758.2|EE163758
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|211377469|gb|FL308234.1|FL308234
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCYTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|148993468|gb|EE033787.2|EE033787
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|50329231|gb|CO524357.1|CO524357
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|211276077|gb|FL337059.1|FL337059
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|211241657|gb|FL328636.1|FL328636
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|5398723|gb|AI812188.1|AI812188
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|211290848|gb|FL314519.1|FL314519
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
EST: gi|50331822|gb|CO526948.1|CO526948
EST:     CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAG                         GGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG
genomic: CCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAG

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: 41

CGTCGCCTCCTCTGGCGTCGCGTCCTGCTCCCTGCGCGCCGGCGGCGACTCCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAGGTGGACGTTGTGACCGAGGATGACAGCGTCGATGGTGACGTTACCGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

CGTCGCCTCCTCTGGCGTCGCGTCCTGCTCCCTGCGCGCCGGCGGCGACTCCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAGGTGGACGTTGTGACCGAGGATGACAGCGTCGATGGTGACGTTACCGACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 7

CGTCGCCTCCTCTGGCGTCGCGTCCTGCTCCCTGCGCGCCGGCGGCGACTCCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAGGTGGACGTTGTGACCGAGGATGACAGCGTCGATGGTGACGTTACCGACG


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 11

CGTCGCCTCCTCTGGCGTCGCGTCCTGCTCCCTGCGCGCCGGCGGCGACTCCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttt ... ttttgatcagGGGGAGGGGACGAGGACACGGAATTGCCCAATATTTCGTTGTGCCAATAAGGTGGACGTTGTGACCGAGGATGACAGCGTCGATGGTGACGTTACCGACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCGCCTCCTCTGGCGTCGCGTCCTGCTCCCTGCGCGCCGGCGGCGACTCCCGGCGGTTTGGCCCCCGACTCGTCCTCCTGCGGAGAGGAGGCGCCGAGgtgagagttttcgtcttccccgtccctcctacctccccttgccattccattacttggtagcttcgaatcgggaggtacttgtctttgtttcgttatctgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG