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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccggtcagatcagatgcagagacggccggtttgtatactccactccaccatctgcacaggttttcagagaccccacctgcttgtttacgtgcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGGAATCCGGCGGCGGGGTCATGCGACGGCAGCAGCTGCTACGGGGGCGACA

Basic information

species Zea mays
transcript GRMZM2G147051_T03
intron # 5
splice site 3'
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|88755336|gb|DY539477.1|DY539477
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GGCCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|32795426|gb|CD947662.1|CD947662
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|71762919|gb|DR960856.1|DR960856
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|31909293|gb|CD650846.1|CD650846
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|211261971|gb|FK957243.1|FK957243
EST:     CTCGAAGTCGACGACTTCCCGTATCCTTAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: CTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|110532757|gb|EE036937.1|EE036937
EST:     TGGGGCACGTAATCCACATGCTGGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|32808949|gb|CD961183.1|CD961183
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCTCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|149061074|gb|EE157329.2|EE157329
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|71308371|gb|DR790412.1|DR790412
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|29544270|gb|CB604650.1|CB604650
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|211021101|gb|FL442869.1|FL442869
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|31909329|gb|CD650864.1|CD650864
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|30088116|gb|CB886321.1|CB886321
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|60359282|gb|DN226255.1|DN226255
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|71315684|gb|DR794463.1|DR794463
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|31909517|gb|CD650958.1|CD650958
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|50337020|gb|CO532146.1|CO532146
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|93280862|gb|EB673126.1|EB673126
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAATTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|91878715|gb|EB408672.1|EB408672
EST:     TGGGGCAGGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|28987043|gb|CB351436.1|CB351436
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|71315686|gb|DR794464.1|DR794464
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|37396493|gb|CF635537.1|CF635537
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|32799292|gb|CD951528.1|CD951528
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|28910805|gb|CB331622.1|CB331622
EST:     TGGGGCCCGTAATCCCCATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAAC
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAAC
EST: gi|4646607|gb|AI491416.2|AI491416
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|32799005|gb|CD951241.1|CD951241
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCGACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|211492061|gb|FL444499.1|FL444499
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|71439998|gb|DR821048.1|DR821048
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|71308861|gb|DR790680.1|DR790680
EST:     TGGGGCACGTAATCCCCATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|74242066|gb|DT649980.1|DT649980
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|211261970|gb|FK957242.1|FK957242
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|4681206|gb|AI629876.1|AI629876
EST:     ATGCTCGAAGTCGACGACTTCCCGTATCGAGAG                         GACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: ATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|88757475|gb|DY541616.1|DY541616
EST:     TGGGGCGCGTAATCCACATGCTCGAAGTGGACGCCTTCCCGTATCGAGAG                         GGCCGTCGAACTTTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG
EST: gi|32789815|gb|CD942051.1|CD942051
EST:     TGGGGCACGTAATCCACATGCTCGAAGTCGACGCCTTCCCGTATCGAGAG                         GATCGTCGAACTCTTCGGCCGGGCACCGGCAGCCCCCTGGAGAAGGCGAGG
genomic: TGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGG

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: 65

CCTGGTCGCGCTGAGGTGCGTGGATCCCGACTCGCAGAAACGGCCCAAGATGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGGAATCCGGCGGCGGGGTCATGCGACGGCAGCAGCTGCTACGGGGGCGACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 26

CCTGGTCGCGCTGAGGTGCGTGGATCCCGACTCGCAGAAACGGCCCAAGATGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGGAATCCGGCGGCGGGGTCATGCGACGGCAGCAGCTGCTACGGGGGCGACA


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 6

CCTGGTCGCGCTGAGGTGCGTGGATCCCGACTCGCAGAAACGGCCCAAGATGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGGAATCCGGCGGCGGGGTCATGCGACGGCAGCAGCTGCTACGGGGGCGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 29

CCTGGTCGCGCTGAGGTGCGTGGATCCCGACTCGCAGAAACGGCCCAAGATGGGGCACGTAATCCACATGCTCGAAGTCGACGACTTCCCGTATCGAGAGgtgagccctg ... gcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGGAATCCGGCGGCGGGGTCATGCGACGGCAGCAGCTGCTACGGGGGCGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccatctgcacaggttttcagagaccccacctgcttgtttacgtgcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGGAATCCGGCGGCGGGGTCATGCGACGGCAGCAGCTGCTACGGGGGCGACA
                                            tgcttct  CT-rich tract
                                   ttgttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccggtcagatcagatgcagagacggccggtttgtatactccactccaccatctgcacaggttttcagagaccccacctgcttgtttacgtgcttctgcagGACCGTCGAACTCTTCGGCCGGGCAACGGCAGCCCCCTGGAGAAGGCGAGGAATCCGGCGGCGGGGTCATGCGACGGCAGCAGCTGCTACGGGGGCGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT