Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTCGGCCTGCGGCTCTCGTTCCGCGCGGCGGCAGCGAGAGCATCACCGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttctttttaatttcctccaagggtcccaatcaatctcaaccttctcttgcacttctttttatattgttgtttctttgcaaacgagccattgagtatcatgtgctctaatgtgctcgtatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g55570.1
intron # 1
splice site 5'
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|33818625|gb|CF335136.1|CF335136
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88696545|gb|CI740120.1|CI740120
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|33813231|gb|CF332506.1|CF332506
EST:     TCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: TCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88346141|gb|CI634014.1|CI634014
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|55409935|gb|CV722311.1|CV722311
EST:     GGGAATCTCCCCATGCTGTCTTG-TTTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: GGGAATCTCCCCATGCTG-CCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88573876|gb|CI665645.1|CI665645
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|14714366|gb|AU198287.1|AU198287
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|33813229|gb|CF332505.1|CF332505
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|33681227|gb|CF309466.1|CF309466
EST:     CCCCATACTGCCTGCAGTGCCAAGCACCAGATTTG-TTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|33666134|gb|CF297101.1|CF297101
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|86903736|gb|CI300590.1|CI300590
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|38479869|gb|CF963958.1|CF963958
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|55410151|gb|CV722527.1|CV722527
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|33681228|gb|CF309467.1|CF309467
EST:     CGGGAATCTCCCCATACTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88988709|gb|CI039128.1|CI039128
EST:     TGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: TGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88979318|gb|CI025820.1|CI025820
EST:     CAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88348094|gb|CI637555.1|CI637555
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|38476046|gb|CF960179.1|CF960179
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88574306|gb|CI666075.1|CI666075
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGC-AATGTCGTCGCTGCAAAGGCTGCGCAGGACAGT
EST: gi|29686441|gb|CB682716.1|CB682716
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|33824040|gb|CF337833.1|CF337833
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACGGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88342540|gb|CI637116.1|CI637116
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88368616|gb|CI648094.1|CI648094
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|58590453|gb|CF988761.1|CF988761
EST:     GGGAATCTCCCCATGCTGCCTGCAGTGCCCAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGGTCTGCAATGTCTGTCGCTGCAAAGGCTGCGCAGGACA
genomic: GGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGA-GTC-GCAATGTC-GTCGCTGCAAAGGCTGCGCAGGACA
EST: gi|117225508|gb|CT859158.1|CT859158
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|88296188|gb|CI667578.1|CI667578
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|58587351|gb|CF985659.1|CF985659
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|33672558|gb|CF300797.1|CF300797
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
EST: gi|33677215|gb|CF305454.1|CF305454
EST:     CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAG                         GGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT
genomic: CGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTT

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: 71 (upstream exon), 75 (downstream exon)
Score: 48

GTTGCTCGGCCTGCGGCTCTCGTTCCGCGCGGCGGCAGCGAGAGCATCACCGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttct ... tcgtatgcagGGAGGATGAGGAGTCGCAATGTCGTCGCTGCAAAGGCTGCGCAGGACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTCGGCCTGCGGCTCTCGTTCCGCGCGGCGGCAGCGAGAGCATCACCGGGAATCTCCCCATGCTGCCTGCAGTGCCAAGCACCAGATTTGTTTCAGgtgtttttctttttaatttcctccaagggtcccaatcaatctcaaccttctcttgcacttctttttatattgttgtttctttgcaaacgagccattgagtatcatgtgctctaatgtgctcgtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG