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

TACCTGCGGGTCGCCCCAGCCGGCCACCCGCGCCCCCGCACCCTACTGACTTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgactggtttgtgagtaatggactatttattgatttctagtttccatccactgtatattcgcattctgaaattctcttcaaaaaatgccaaagtg...

Basic information

species Zea mays
transcript GRMZM2G017584_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|211059012|gb|FL008172.1|FL008172
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|91057050|gb|EB167468.1|EB167468
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|31909681|gb|CD651040.1|CD651040
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAAGCTG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAA-GCTG
EST: gi|32798166|gb|CD950402.1|CD950402
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTA
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTA
EST: gi|211059010|gb|FL008170.1|FL008170
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|93014337|gb|EB639857.1|EB639857
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|71326301|gb|DR799839.1|DR799839
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|211059016|gb|FL008176.1|FL008176
EST:     TTGGGCTTGCTGTATAGCACGGACCACATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|211059013|gb|FL008173.1|FL008173
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|148954016|gb|EC899414.2|EC899414
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|86469976|gb|DY236346.1|DY236346
EST:     TTGGGTTTGCTGTATAGCACGGACCAAATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|211059011|gb|FL008171.1|FL008171
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|78116765|gb|DV535152.1|DV535152
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|30087147|gb|CB885355.1|CB885355
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|211059014|gb|FL008174.1|FL008174
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
EST: gi|31910413|gb|CD651411.1|CD651411
EST:     TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACG                         TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG
genomic: TTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGG

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: 44 (upstream exon), 49 (downstream exon)
Score: 42

TACCTGCGGGTCGCCCCAGCCGGCCACCCGCGCCCCCGCACCCTACTGACTTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG


Block sizes: 39 (upstream exon), 40 (downstream exon)
Score: 13

TACCTGCGGGTCGCCCCAGCCGGCCACCCGCGCCCCCGCACCCTACTGACTTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 8

TACCTGCGGGTCGCCCCAGCCGGCCACCCGCGCCCCCGCACCCTACTGACTTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 13

TACCTGCGGGTCGCCCCAGCCGGCCACCCGCGCCCCCGCACCCTACTGACTTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgact ... tcttatacagTTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCTGCGGGTCGCCCCAGCCGGCCACCCGCGCCCCCGCACCCTACTGACTTGGGCTTGCTGTATAGCACGGACCAGATCAAGGGTCGTCGTCGACCACGgtgagtgactggtttgtgagtaatggactatttattgatttctagtttccatccactgtatattcgcattctgaaattctcttcaaaaaatgccaaagtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaaaaa