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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGGCAGCTCCGAGCAGGGTCGTCGTCTGCTCCGTCGCGTCTACCGAGGGGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacgaaatgacaaggctggcaggcgcgggcacagggcatcggtgggagagctttggttgggattaagactgaacttggttacttgtgctggtgtgaaatgcag

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g17120.2 (Oryza sativa), 5'ss of exon 1
CCGGGC-AGCTCCGAGCAGGGTCGTCGTCTGCTCCGTCGCGTCTACCGAGGGGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacgaaatgacaaggctggcaggcgcgggcacagggcatcggtgggagagctttggttgggattaagactgaacttggttacttgtgctggtgtgaaatgcag
|||| | |||||   || |       |  || || | |||  || |||||||||| |||||||| |||||||||||||||||||| ||||| ||||| ||||||  | ||    |  |   |  | |  ||| ||||   ||||   ||         |||   |  | | ||    |    ||||| ||  | | |||| |   | |||
CCGGACGAGCTCTCCGCGGCCATCCAGGATGGTCTG-CGCCGCTGCCGAGGGGTTTATCTCCGCGGCGCCGATCCTCCTCCCCGACGGCCCGTGGAAGCAGgtgggtaactggtttccggtgaagcc--gcgggggcgttgggctgtgggtttttttttttcagtatgctgaatctggtggctggttgctgat-cgggtgcgggtt-cag
















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|89755796|gb|DY686083.1|DY686083
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|71298836|gb|DR785405.1|DR785405
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|74242073|gb|DT649987.1|DT649987
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|149095151|gb|EE180766.2|EE180766
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|148956344|gb|EC902151.2|EC902151
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|148938791|gb|EC883128.2|EC883128
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|78092275|gb|DV520649.1|DV520649
EST:     CTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: CTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|149000193|gb|EE037335.2|EE037335
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|149009106|gb|EE041258.2|EE041258
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCCATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|148932140|gb|EC875563.2|EC875563
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|211328123|gb|FL062397.1|FL062397
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGAGGGCCCTTGGAMACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|211453339|gb|FL002421.1|FL002421
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|28873422|gb|CB329414.1|CB329414
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GCGGAAGGCGGCGGCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|149071265|gb|EE159660.2|EE159660
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|71446471|gb|DR827521.1|DR827521
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|148930889|gb|EC873334.2|EC873334
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|148972816|gb|EE023801.2|EE023801
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGCGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|149110343|gb|EE190365.2|EE190365
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|20301290|gb|BQ164233.1|BQ164233
EST:     GGTTCATCTCCTTAGCGCCGATCCTCCTCCCCGAGGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|211328125|gb|FL062399.1|FL062399
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGAGGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
EST: gi|149084216|gb|EE173633.2|EE173633
EST:     GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAG                         GTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC
genomic: GGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 295

CCGGGCAGCTCCGAGCAGGGTCGTCGTCTGCTCCGTCGCGTCTACCGAGGGGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 278

CCGGGCAGCTCCGAGCAGGGTCGTCGTCTGCTCCGTCGCGTCTACCGAGGGGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 236

CCGGGCAGCTCCGAGCAGGGTCGTCGTCTGCTCCGTCGCGTCTACCGAGGGGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 105

CCGGGCAGCTCCGAGCAGGGTCGTCGTCTGCTCCGTCGCGTCTACCGAGGGGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacg ... tgaaatgcagGTGGAAGGCGGCGTCACTGCCGCGAAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGGCAGCTCCGAGCAGGGTCGTCGTCTGCTCCGTCGCGTCTACCGAGGGGTTCATCTCCGCAGCGCCGATCCTCCTCCCCGATGGCCCTTGGAAACAGgtgactgacgaaatgacaaggctggcaggcgcgggcacagggcatcggtgggagagctttggttgggattaagactgaacttggttacttgtgctggtgtgaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC