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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacccttgcgctcgattcgtttagtgatgggaacttttcgaagtccttggctttgtcgtggtggatatttaactcggggattttttcctgtcttccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGCCAAGTCTTTGACTCCCAAGGCGAAGCTGCCGGCCATCGGTGGTGACACC

Basic information

species Zea mays
transcript GRMZM2G702026_T01
intron # 13
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|211139203|gb|FL356418.1|FL356418
EST:     TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAG                         TGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
genomic: TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
EST: gi|211162598|gb|FL365710.1|FL365710
EST:     TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAG                         TGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGG
genomic: TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGG
EST: gi|86466103|gb|DY232476.1|DY232476
EST:     TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAG                         TGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
genomic: TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
EST: gi|71310429|gb|DR791520.1|DR791520
EST:     TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAG                         TGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCTTACGAGGAGGC
genomic: TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
EST: gi|86466142|gb|DY232515.1|DY232515
EST:     TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAG                         TGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
genomic: TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
EST: gi|149099574|gb|EE185613.2|EE185613
EST:     TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAG                         TGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
genomic: TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
EST: gi|26457668|gb|CA829251.1|CA829251
EST:     TACACAGACGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAG                         TGAGTTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
genomic: TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
EST: gi|22543313|gb|BU093751.1|BU093751
EST:     TACACAGACGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAG                         TGAGTTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC
genomic: TACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGC

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: 172

TCGATATCCCGGGAGAGCTTTCCGCCAGCCTCAAGAAATGGAAGGTGATCTACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGCCAAGTCTTTGACTCCCAAGGCGAAGCTGCCGGCCATCGGTGGTGACACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

TCGATATCCCGGGAGAGCTTTCCGCCAGCCTCAAGAAATGGAAGGTGATCTACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGCCAAGTCTTTGACTCCCAAGGCGAAGCTGCCGGCCATCGGTGGTGACACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

TCGATATCCCGGGAGAGCTTTCCGCCAGCCTCAAGAAATGGAAGGTGATCTACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGCCAAGTCTTTGACTCCCAAGGCGAAGCTGCCGGCCATCGGTGGTGACACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 97

TCGATATCCCGGGAGAGCTTTCCGCCAGCCTCAAGAAATGGAAGGTGATCTACACAGATGACGAGGACGATATGATGCTGGTCGGGGACGATCCATGGAGgtatgtaccc ... tccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGCCAAGTCTTTGACTCCCAAGGCGAAGCTGCCGGCCATCGGTGGTGACACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctttgtcgtggtggatatttaactcggggattttttcctgtcttccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGCCAAGTCTTTGACTCCCAAGGCGAAGCTGCCGGCCATCGGTGGTGACACC
                  atttaac  putative branch site (score: 97)
                                ttttttcctgtcttcc  putative PPT
                atatttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacccttgcgctcgattcgtttagtgatgggaacttttcgaagtccttggctttgtcgtggtggatatttaactcggggattttttcctgtcttccgttgcagTGAATTTTGCAGGATGGTAAAAAGGATATACATTTATTCCTACGAGGAGGCCAAGTCTTTGACTCCCAAGGCGAAGCTGCCGGCCATCGGTGGTGACACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC