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

gtaaataaaccaattctaaagctatttctgattgatattttaggtccaaatgtattatattttgttgtcatgtggtggaaactctggttacgaatgttcttgttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGATCATCCCAGGGAGGGTGGTTTTGTACCTGTCACATTGAACAGCGGTGGAT

Basic information

species Zea mays
transcript GRMZM2G069009_T01
intron # 3
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|78082473|gb|DV510885.1|DV510885
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|94476471|gb|EB705429.1|EB705429
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|149005039|gb|EE039564.2|EE039564
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|91049855|gb|EB160273.1|EB160273
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|148956932|gb|EC902865.2|EC902865
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|149094715|gb|EE180267.2|EE180267
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|78082860|gb|DV511253.1|DV511253
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGGACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|71418361|gb|DR804412.1|DR804412
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|76937022|gb|DV175010.1|DV175010
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|74232341|gb|DT640255.1|DT640255
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|149087101|gb|EE176640.2|EE176640
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|76286604|gb|DV026172.1|DV026172
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
EST: gi|149102933|gb|EE288285.2|EE288285
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAAT
EST: gi|78114960|gb|DV533348.1|DV533348
EST:     CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG                         TACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT
genomic: CCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGAT

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: 251

GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGATCATCCCAGGGAGGGTGGTTTTGTACCTGTCACATTGAACAGCGGTGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGATCATCCCAGGGAGGGTGGTTTTGTACCTGTCACATTGAACAGCGGTGGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 226

GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGATCATCCCAGGGAGGGTGGTTTTGTACCTGTCACATTGAACAGCGGTGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAGgtaaataaac ... ttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGATCATCCCAGGGAGGGTGGTTTTGTACCTGTCACATTGAACAGCGGTGGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgttgtcatgtggtggaaactctggttacgaatgttcttgttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGATCATCCCAGGGAGGGTGGTTTTGTACCTGTCACATTGAACAGCGGTGGAT
                                       ttcttgttattttc  CT-rich tract
                                          ttgttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataaaccaattctaaagctatttctgattgatattttaggtccaaatgtattatattttgttgtcatgtggtggaaactctggttacgaatgttcttgttattttcagTACTATGCAAAGAATGGCACCTGTAAATTTGGTTCCAATTGCAAGTTTGATCATCCCAGGGAGGGTGGTTTTGTACCTGTCACATTGAACAGCGGTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA