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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttggttctcgacttctcgtaccactctagtagctttcaatattgaatgcttgatggccacagttgtcctcacttgcgttgtttgtttgataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCATCATTTCTCAGGTGGTGCAAAACTTTCATCAGCCGCCCTTCCAGCGAAAG

Basic information

species Zea mays
transcript GRMZM2G118917_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118917_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os10g30100.1 (Oryza sativa), 3'ss of exon 13
---ttttggttctcgacttctcgtaccactctagtagctttcaatattgaatgcttgatggccacagttgtcctcacttgcgttgtttgtttgataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCATCATTTCTCAGGTGGTGCAAAACTTTCATCAGCCGCCCTTCCAGCGAAAG------
   ||||||  |   |  || |       ||   |   ||||  |    || || |     ||| ||    ||| |||  | |    | | | | || | |||  || |      |||||||||||||  ||||| |||| ||||||||| ||| ||||||  || |||||||||  | |  |  |   | |||||  | |||      
cacttttggaacaaaaagtcactagttcttcccat---tttcctttggaaaagcctagaaaccagagcaaccctgactaacctcagatctgttaaaattgcagAATATG------GTGGACAAGATAAAATCTTCAGTGGCACTTCCTTTCCATAATTTCTGTGGCGGTGCAAAATCTCCGGCCACTAGCATTCCATTGGAAGAATCAG
















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|32933312|gb|CF038124.1|CF038124
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGT
EST: gi|211340621|gb|FL361359.1|FL361359
EST:     GCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
genomic: GCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
EST: gi|60337067|gb|DN204040.1|DN204040
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
EST: gi|26456572|gb|CA828155.1|CA828155
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
EST: gi|211193425|gb|FL343339.1|FL343339
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
EST: gi|20301496|gb|BQ164439.1|BQ164439
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTGCAT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
EST: gi|211301949|gb|FL333158.1|FL333158
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
EST: gi|78108318|gb|DV526736.1|DV526736
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
EST: gi|60396058|gb|DN228927.1|DN228927
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCAT
EST: gi|211248404|gb|FL329614.1|FL329614
EST:     CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAG                         GGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACT
genomic: CAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACT

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), 48 (downstream exon)
Score: 239

TGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCATCATTTCTCAGGTGGTGCAAAACTTTCATCAGCCGCCCTTCCAGCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCATCATTTCTCAGGTGGTGCAAAACTTTCATCAGCCGCCCTTCCAGCGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 135

TGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCATCATTTCTCAGGTGGTGCAAAACTTTCATCAGCCGCCCTTCCAGCGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGATTTTCAAATGTTCAGgtattatcta ... ataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCATCATTTCTCAGGTGGTGCAAAACTTTCATCAGCCGCCCTTCCAGCGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgcttgatggccacagttgtcctcacttgcgttgtttgtttgataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCATCATTTCTCAGGTGGTGCAAAACTTTCATCAGCCGCCCTTCCAGCGAAAG
                                           tgataac  putative branch site (score: 134)
                                         tttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttggttctcgacttctcgtaccactctagtagctttcaatattgaatgcttgatggccacagttgtcctcacttgcgttgtttgtttgataacttcagGGTAAGACTAAGGTGGACAAGATAACGTCTTCCGTGGTACTTCCTTTTCATCATTTCTCAGGTGGTGCAAAACTTTCATCAGCCGCCCTTCCAGCGAAAG

- -tggttct
- - - - - - - - - -gtaccac
- - - - - - - - - - - - - - - - - - - - - - tgaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt