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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtagagattattttgatcatgacagttttgtacttcagcgacctgtgatactgagaaaacaataggcgaatattttgaatgtgacctatgatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAATAGCTGCAGGTATAGTGGAAGGCATGAGTCTCGGGAACAACTGTATGGCT

Basic information

species Zea mays
transcript GRMZM2G063258_T04
intron # 5
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|87154557|gb|DY399346.1|DY399346
EST:     TCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAG                         TGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
genomic: TCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
EST: gi|94479866|gb|EB708824.1|EB708824
EST:     GCATCCCCAAATTTGGGGATAAGCACATCAAG                         TGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
genomic: GCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
EST: gi|21330849|gb|BQ486230.1|BQ486230
EST:     AGGATAAGCACATCAAG                         TGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
genomic: AGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
EST: gi|71330652|gb|DR802102.1|DR802102
EST:     TCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAG                         TGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
genomic: TCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
EST: gi|91870595|gb|EB400977.1|EB400977
EST:     TCTGTTCAACAACTGTTAGCATCCCCCAATTTGAGGATAAGCACATCAAG                         TGATGTTACAGGAGTAGAAATCGCAAGTGCCCT
genomic: TCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCT
EST: gi|26455233|gb|CA826816.1|CA826816
EST:     TCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAG                         TGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT
genomic: TCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAAT

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), 44 (downstream exon)
Score: 7

CAATGGTGGTGGCATCCAAAGACAACAAGTTGGCAAGTTCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAATAGCTGCAGGTATAGTGGAAGGCATGAGTCTCGGGAACAACTGTATGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 15

CAATGGTGGTGGCATCCAAAGACAACAAGTTGGCAAGTTCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAATAGCTGCAGGTATAGTGGAAGGCATGAGTCTCGGGAACAACTGTATGGCT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 5

CAATGGTGGTGGCATCCAAAGACAACAAGTTGGCAAGTTCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAATAGCTGCAGGTATAGTGGAAGGCATGAGTCTCGGGAACAACTGTATGGCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 14

CAATGGTGGTGGCATCCAAAGACAACAAGTTGGCAAGTTCTGTTCAACAACTGTTAGCATCCCCAAATTTGAGGATAAGCACATCAAGgtaaaattgc ... gatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAATAGCTGCAGGTATAGTGGAAGGCATGAGTCTCGGGAACAACTGTATGGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatactgagaaaacaataggcgaatattttgaatgtgacctatgatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAATAGCTGCAGGTATAGTGGAAGGCATGAGTCTCGGGAACAACTGTATGGCT
                        aatattttgaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtagagattattttgatcatgacagttttgtacttcagcgacctgtgatactgagaaaacaataggcgaatattttgaatgtgacctatgatacttcagTGATGTTACAGGAGTAGAAATCGCAGGTGCCCTGAAGAACGTTCTTGCAATAGCTGCAGGTATAGTGGAAGGCATGAGTCTCGGGAACAACTGTATGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG