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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgtatgtcatgacattgacacccagtgattgctggctaagcgtttcctctattcgtatctcaatccaaggtctaactgaagctacacaatttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG

Basic information

species Zea mays
transcript GRMZM2G461569_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 15
lower sequence: 13114.m00152 (Oryza sativa), 3'ss of exon 4
-------ccgtatgtcatgacattgacacccagtgattgctggctaagcgtttcctctattcgtatctcaatccaaggtctaactgaagctacacaatttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG
       | | || |  | |  |  |     |    |||||  || | | |        || || | || || ||   | |   ||    |      |||||  ||||||||||||||||||||||||||| |||||||||| |||||||| || || ||||||||| ||||| ||||||| ||||| |||||||| ||||| ||||
tttcctactggattttcttaactgaaagggaaaaacttgctaactgatcatacttctctttagtttttctattcataatttt-ttggtttt------tttttttcagGTGGGAAAATTAGCTGACCTTGTTATTTGGAAACCTTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGG

upper sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 15
--ccgtatgtcatgacattga-cacccagtgattgctggctaagcgtttcctctattcgtatctcaatccaaggtctaactgaagctacacaatttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG
    || |||  | |||  || ||  |  || || |   |   | ||| | |     |  |  |   | |  |  ||   ||  |   |     |||  ||||||||| ||  | ||||| |||||||| ||||| ||||||||||| || || ||||||||| ||||  |||| || |||| ||||||||||||||||||||
gcttgtgtgtgtttacagagatcatactctggtt-ccacccttgagttacatta--ccaaaattgtttactcgtccttgatgttgtatcttgtgtttccacagGTGGGGAAGGTGGCTGATCTTGTTCTCTGGAATCCATCTTTCTTTGGGGCAAAACCAGAAATGGTGATAAAAGGTGGTGTAATTGCATGGGCTAACATGG
















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|211109878|gb|FL467775.1|FL467775
EST:     TCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTYTTCGGCGCT
genomic: TCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|32834778|gb|CD974456.1|CD974456
EST:     TAAATCCAGCAATAGTGAACGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|32932810|gb|CF037622.1|CF037622
EST:     TAAATCCAGCAATAGTGAACGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|213172274|gb|FM186421.1|FM186421
EST:     TAAATCCAGCAATAGTGAACGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|213172803|gb|FM187184.1|FM187184
EST:     TAAATCCAGCAATAGTGAACGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|76011931|gb|DT939101.1|DT939101
EST:     TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|31358228|gb|CD442585.1|CD442585
EST:     GCAATAGTGAACGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: GCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|32834768|gb|CD974446.1|CD974446
EST:     TAAATCCAGCAATAGTGAACGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|32835420|gb|CD975098.1|CD975098
EST:     TAAATCCAGCAATAGTGAACGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|213170447|gb|FM190520.1|FM190520
EST:     TAAATCCAGCAATAGTGAACGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|211090509|gb|FK961026.1|FK961026
EST:     TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTARCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
genomic: TAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCT
EST: gi|78085739|gb|DV514132.1|DV514132
EST:     AATCCCAGCA-TAGTGAAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAG                         GTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTT
genomic: AATCC-AGCAATAGTGAA-TGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTT

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: 119

CCCGGACAGTGACAACCTCCGTATAAGAAGATACATAGCAAAATACACAATAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 162

CCCGGACAGTGACAACCTCCGTATAAGAAGATACATAGCAAAATACACAATAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

CCCGGACAGTGACAACCTCCGTATAAGAAGATACATAGCAAAATACACAATAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

CCCGGACAGTGACAACCTCCGTATAAGAAGATACATAGCAAAATACACAATAAATCCAGCAATAGTGAATGGGTTTTCAGACTTTGTTGGTTCTGTTGAGgtatgtctta ... tttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctattcgtatctcaatccaaggtctaactgaagctacacaatttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG
                         gtctaac  putative branch site (score: 114)
                                             ttttt  putative PPT
                                         acaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgtatgtcatgacattgacacccagtgattgctggctaagcgtttcctctattcgtatctcaatccaaggtctaactgaagctacacaatttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG

- - -tgtcatg
- - - - - - - - - - - - - - - tgctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacacaa