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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCGCCGCCGAATCCGAGACTCTGATCTCGGGTTCACCGCAGCGCACAGAGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtctcctccggatctcttgctgcctcgcttgttattccgttgcttttcggtgtccgatctgccgcggcggtgggtctcggtccatctggcggcg...

Basic information

species Zea mays
transcript GRMZM2G027995_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|211082279|gb|FL286148.1|FL286148
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|211079538|gb|FL286131.1|FL286131
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|8368624|gb|BE051569.1|BE051569
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|31354357|gb|CD438714.1|CD438714
EST:     AGCACCCCTGACTCCCGGCCCGATCTGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|32851137|gb|CD990818.1|CD990818
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|67041361|gb|CO467616.1|CO467616
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|211288318|gb|FL286178.1|FL286178
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|211294754|gb|FL286234.1|FL286234
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|28931273|gb|CB334634.1|CB334634
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|31354677|gb|CD439034.1|CD439034
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|31351797|gb|CD436154.1|CD436154
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|31359138|gb|CD443495.1|CD443495
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCGACTAT
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGC-ACTAT
EST: gi|14529473|gb|BI096606.1|BI096606
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|22715433|gb|BU197760.1|BU197760
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|211290464|gb|FL286197.1|FL286197
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|211082280|gb|FL286149.1|FL286149
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|14646056|gb|BI180245.1|BI180245
EST:     ACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: ACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|20811047|gb|BQ295525.1|BQ295525
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|31356525|gb|CD440882.1|CD440882
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TC-TTCCTTGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTAT
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGC-AGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTAT
EST: gi|31349540|gb|CD433897.1|CD433897
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|8368623|gb|BE051568.1|BE051568
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCGTGGG                         TCTTTGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|32933398|gb|CF038210.1|CF038210
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|30306982|gb|CD001655.1|CD001655
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|31353577|gb|CD437934.1|CD437934
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCCACGCTACAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|32851113|gb|CD990794.1|CD990794
EST:     AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
EST: gi|67017759|gb|CO446508.1|CO446508
EST:     AGCACCCCCGACTCCCGTCCCGATCCGCGCTCTCCTCTACGACGCTTCAG                         TCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG
genomic: AGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATG

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: 48 (upstream exon), 49 (downstream exon)
Score: 321

CTCCGCCGCCGAATCCGAGACTCTGATCTCGGGTTCACCGCAGCGCACAGAGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATGATTCTAAAATGCAGGAGCTGCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 117

CTCCGCCGCCGAATCCGAGACTCTGATCTCGGGTTCACCGCAGCGCACAGAGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATGATTCTAAAATGCAGGAGCTGCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 85

CTCCGCCGCCGAATCCGAGACTCTGATCTCGGGTTCACCGCAGCGCACAGAGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATGATTCTAAAATGCAGGAGCTGCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 114

CTCCGCCGCCGAATCCGAGACTCTGATCTCGGGTTCACCGCAGCGCACAGAGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtct ... tttgctacagTCATGGCAGGAATGGCACCCGAGGGTTCTCAGTTTGATGCTAAGCACTATGATTCTAAAATGCAGGAGCTGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCGCCGCCGAATCCGAGACTCTGATCTCGGGTTCACCGCAGCGCACAGAGCACCCCTGACTCCCGGCCCGATCCGCGCTCTCCTCTCCGACGCTTCAGgtggtcgtctcctccggatctcttgctgcctcgcttgttattccgttgcttttcggtgtccgatctgccgcggcggtgggtctcggtccatctggcggcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgcctc