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'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgggcatatgctaattttcaccggtgcatgtgacactagagtcatgcaattgtttatcatgttacttttgttgtttaacatatttatttcatcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCAGATTTACGTGGACCATTGAAGATTTTTCGAATCACAGAAAGCTGTACTC

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 2
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|88390787|gb|CI611013.1|CI611013
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88402176|gb|CI615019.1|CI615019
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTA-GTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|86904504|gb|CI308714.1|CI308714
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88718957|gb|CI742467.1|CI742467
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88311790|gb|CI577396.1|CI577396
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88453182|gb|CI563422.1|CI563422
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88692071|gb|CI735646.1|CI735646
EST:     GCTGGTGCCAGGCCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88315847|gb|CI617320.1|CI617320
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAAC-TCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88371255|gb|CI597732.1|CI597732
EST:     GCTGGTGCCAGAACAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTAACAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88298888|gb|CI567891.1|CI567891
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88723755|gb|CI747265.1|CI747265
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
EST: gi|88372041|gb|CI609949.1|CI609949
EST:     GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAG                         ACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA
genomic: GCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCA

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 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 72 (downstream exon)
Score: 47

CTCCTGCAGCAGGACCAGGATGAGGAGATGCTGGTGCCAGACCAGGATGTTGTTGTTGAGGGACCTCAGCCGATGGAAGgtgagatttc ... catcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCAGATTTACGTGGACCATTGAAGATTTTTCGAATCACAGAAAGCTGTACTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaattgtttatcatgttacttttgttgtttaacatatttatttcatcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCAGATTTACGTGGACCATTGAAGATTTTTCGAATCACAGAAAGCTGTACTC
                            gtttaac  putative branch site (score: 47)
                                          tttcatctt  putative PPT
                 ttacttttgttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgggcatatgctaattttcaccggtgcatgtgacactagagtcatgcaattgtttatcatgttacttttgttgtttaacatatttatttcatcttgcagACTCTGGATCAACAGTTGAGAACGAGCAGGTACCAGAAACCTCTACGTCCAGATTTACGTGGACCATTGAAGATTTTTCGAATCACAGAAAGCTGTACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - -catatgc
- - - - - - - - -ttcaccg
- - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgttt