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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcacagtcgttttttttttttttttgcaaggtaaatcaccctgcagttatatgcgattttcactggttctgatgcttgtttgcccacttttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCATAATTGTTGTCAGCCCGAAGGGGGTGATCTCTTTTATGTCTCGGATCCAC

Basic information

species Oryza sativa
transcript LOC_Os01g24750.1
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|86834597|gb|CI340714.1|CI340714
EST:     CTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: CTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|86892837|gb|CI312133.1|CI312133
EST:     AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|88833870|gb|CI077351.1|CI077351
EST:     AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCTAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|38470216|gb|CF954347.1|CF954347
EST:     AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|29640983|gb|CB645990.1|CB645990
EST:     AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|86496476|gb|CI139109.1|CI139109
EST:     AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|58688011|gb|CK076698.1|CK076698
EST:     GGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: GGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|88834000|gb|CI077481.1|CI077481
EST:     AGCCAAATGATACAGGGGCTCCGCATTCAAGGAAACCAACTTCGAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|86496183|gb|CI138816.1|CI138816
EST:     AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|86901338|gb|CI326181.1|CI326181
EST:     TTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: TTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|29614158|gb|CB619171.1|CB619171
EST:     AGCCAAATGATACGGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|88227508|gb|CI226988.1|CI226988
EST:     AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACTAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|86879329|gb|CI327083.1|CI327083
EST:     CATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: CATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
EST: gi|29669872|gb|CB666147.1|CB666147
EST:     AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAG                         ACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT
genomic: AGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCAT

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: 52 (upstream exon), 70 (downstream exon)
Score: 14

TGCTCTGTTGAGCATAGATGAAAGTTTAATGTGTTCTTTTCAAATCTTGAAGCCAAATGATACAGGGGCTCCACATTCAAGGAAACCAACTTCAAACAAGgtaaaatatc ... tttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCATAATTGTTGTCAGCCCGAAGGGGGTGATCTCTTTTATGTCTCGGATCCAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttatatgcgattttcactggttctgatgcttgtttgcccacttttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCATAATTGTTGTCAGCCCGAAGGGGGTGATCTCTTTTATGTCTCGGATCCAC
                       ttctgat  putative branch site (score: 14)
                                   tttgcccactttttt  putative PPT
                                          actttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcacagtcgttttttttttttttttgcaaggtaaatcaccctgcagttatatgcgattttcactggttctgatgcttgtttgcccacttttttgacagACCCCAAAAACTGGAAACGCTTAACTTATATTATATCAAGCTACAAAGCATAATTGTTGTCAGCCCGAAGGGGGTGATCTCTTTTATGTCTCGGATCCAC

- - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - -cctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc