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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcaatagttatctagaagatcatatttaccggttggttagacaagttccatttttctgtgtgtctcagttgtgtctaacatcatcatcatgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCTGGATTGAGAGCATTGGCGCTTCTTGGAGTTGGTGCCTCCGGTCTTTTGA

Basic information

species Zea mays
transcript GRMZM2G032367_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032367_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 3
atcaatagttatctagaagatcatatttaccggttggttagacaagttccatttttctgtg-tgtctcagttgtgtctaa--catcatcatcatgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCTGGATTGAGAGCATTGGCGCTTCTTGGAGTTGGTGCCTCCGGTCTTTTGA
  || ||   || | |   | ||||  |  | ||      ||  |  ||| ||||  |||| || |    || | | |||  ||| || |||||| | |||||||  |||  ||||| || || || |||  ||| |||||||| ||||| |||||| ||||||||||||| ||||||||||||||||| || |||||||| |
-acagtaaccattt-gttcaccataagtttcagtacccatgatcatctcctttttagtgtggtgacctgcttttttttaaaacattataatcatg-ttttcagGGCTCATCTCTGCTATCCTCGTTCCGGATAAAGCATGAAGAATCCTCCGCTGGACTGAGAGCATTGGCTCTTCTTGGAGTTGGTGCTTCTGGTCTTTTAA
















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|91048787|gb|EB159205.1|EB159205
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|148953376|gb|EE152870.2|EE152870
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|6127287|gb|AW129812.1|AW129812
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|30705068|gb|CD058657.1|CD058657
EST:     AGGGGCATTAACCAGCTTCTGGAAGGAAAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: AGGGGCATTAACCAGCTTCT-GAA-GAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|101393982|gb|EB818924.1|EB818924
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|88757330|gb|DY541471.1|DY541471
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTTTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|91878167|gb|EB408124.1|EB408124
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|32907328|gb|CF012141.1|CF012141
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|91048031|gb|EB158449.1|EB158449
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|60359697|gb|DN226670.1|DN226670
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|76020657|gb|DT947827.1|DT947827
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|71327453|gb|DR800341.1|DR800341
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|71448913|gb|DR829963.1|DR829963
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|50338207|gb|CO533333.1|CO533333
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|149084255|gb|EE173682.2|EE173682
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|149110785|gb|EE190606.2|EE190606
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
EST: gi|37420962|gb|CF648177.1|CF648177
EST:     CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCT                         GGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT
genomic: CAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCT

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: 118

AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCTGGATTGAGAGCATTGGCGCTTCTTGGAGTTGGTGCCTCCGGTCTTTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCTGGATTGAGAGCATTGGCGCTTCTTGGAGTTGGTGCCTCCGGTCTTTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCTGGATTGAGAGCATTGGCGCTTCTTGGAGTTGGTGCCTCCGGTCTTTTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 181

AGTGCTTGATGGCTGCCGCAAGGGGCATTAACCAGCTTCTGAAGAGAATTCTCCACAACCAGTCCGCTgtaagtgttt ... tgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCTGGATTGAGAGCATTGGCGCTTCTTGGAGTTGGTGCCTCCGGTCTTTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccatttttctgtgtgtctcagttgtgtctaacatcatcatcatgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCTGGATTGAGAGCATTGGCGCTTCTTGGAGTTGGTGCCTCCGGTCTTTTGA
                            gtctaac  putative branch site (score: 181)
                                                tcttc  putative PPT
     atttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcaatagttatctagaagatcatatttaccggttggttagacaagttccatttttctgtgtgtctcagttgtgtctaacatcatcatcatgatcttcagGGTCCATGGCTGCTTTCTTCATTTCGGGGAAATCATGAAGAGTCCTCTGCTGGATTGAGAGCATTGGCGCTTCTTGGAGTTGGTGCCTCCGGTCTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG