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

...ctatagtatgttttgtcttgaacagttaaattgggtttccttgcaaggcatctcatgctatattttagcttacatttgttccttttgttgtccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGCACTGCTTTTGTGAGTCACCATGGGAAGCAGTGGAGCAGATACATCGTCT

Basic information

species Zea mays
transcript GRMZM2G074373_T01
intron # 1
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|93013445|gb|EB638965.1|EB638965
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|211035651|gb|FK982762.1|FK982762
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|8367371|gb|BE050316.1|BE050316
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|211035650|gb|FK982761.1|FK982761
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|71318161|gb|DR795843.1|DR795843
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|78090597|gb|DV518971.1|DV518971
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|148976204|gb|EE025907.2|EE025907
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|94479028|gb|EB707986.1|EB707986
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GATTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|148963993|gb|EE015131.2|EE015131
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|148930175|gb|EC872560.2|EC872560
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|71439024|gb|DR820074.1|DR820074
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
EST: gi|71426949|gb|DR807999.1|DR807999
EST:     ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAG                         GTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC
genomic: ATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGC

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: 200

CAGCTTTACTCTCCCCTCCCGTGTCCAGATCCCGAGGCCCCTCTCCCTCGATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGCACTGCTTTTGTGAGTCACCATGGGAAGCAGTGGAGCAGATACATCGTCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 117

CAGCTTTACTCTCCCCTCCCGTGTCCAGATCCCGAGGCCCCTCTCCCTCGATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGCACTGCTTTTGTGAGTCACCATGGGAAGCAGTGGAGCAGATACATCGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

CAGCTTTACTCTCCCCTCCCGTGTCCAGATCCCGAGGCCCCTCTCCCTCGATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGCACTGCTTTTGTGAGTCACCATGGGAAGCAGTGGAGCAGATACATCGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

CAGCTTTACTCTCCCCTCCCGTGTCCAGATCCCGAGGCCCCTCTCCCTCGATCGCCGCCTCCCGGTAGCGGATCCGGCGCCGGCTCGCGCCCCCCGACAGgtaccctacc ... tccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGCACTGCTTTTGTGAGTCACCATGGGAAGCAGTGGAGCAGATACATCGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcatctcatgctatattttagcttacatttgttccttttgttgtccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGCACTGCTTTTGTGAGTCACCATGGGAAGCAGTGGAGCAGATACATCGTCT
                     agcttac  putative branch site (score: 188)
                                 ttccttttgttgtcc  putative PPT
             tatattttagctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatagtatgttttgtcttgaacagttaaattgggtttccttgcaaggcatctcatgctatattttagcttacatttgttccttttgttgtccaattcagGTTTTGTTTTATGCTTGTTCATTTGTCTATGGACAATGGACTAGTTGCTGCACTGCTTTTGTGAGTCACCATGGGAAGCAGTGGAGCAGATACATCGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT