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

gtaagatcaatccatccaccatctcctgcaaatctcgttgcaacttgcaagcaagaacatcaattgaatctttgttgcttcatctgattaatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACGAGCCAGCAAGCCATGCAGGGACGAAGGCTCAACTACAACTAAATTAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g54590.1
intron # 7
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|86479269|gb|CI121902.1|CI121902
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|89166570|gb|CI103856.1|CI103856
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|87029807|gb|CI274488.1|CI274488
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86597189|gb|CI272784.1|CI272784
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86479542|gb|CI122175.1|CI122175
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86596859|gb|CI270655.1|CI270655
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86834427|gb|CI344372.1|CI344372
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86478625|gb|CI121258.1|CI121258
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|88508865|gb|CI436371.1|CI436371
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86500810|gb|CI143443.1|CI143443
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|87014848|gb|CI271447.1|CI271447
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|88474094|gb|CI411365.1|CI411365
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86479127|gb|CI121760.1|CI121760
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|88259042|gb|CI363335.1|CI363335
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86596935|gb|CI270731.1|CI270731
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|87022932|gb|CI269868.1|CI269868
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|89163864|gb|CI100754.1|CI100754
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTNATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|89165312|gb|CI102402.1|CI102402
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|87027137|gb|CI278169.1|CI278169
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86858330|gb|CI271180.1|CI271180
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86479354|gb|CI121987.1|CI121987
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86477942|gb|CI120575.1|CI120575
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|87027492|gb|CI272257.1|CI272257
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGAC-AACC                         GATATGGCGATTGAGCACAGCGTAGGGAGTTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86828329|gb|CI276898.1|CI276898
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|89163401|gb|CI100291.1|CI100291
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|86827814|gb|CI272988.1|CI272988
EST:     GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGTTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
EST: gi|66918972|gb|CX105820.1|CX105820
EST:     GCTCGCCATACAACAGCAACGCCTCCATGCAGCAACCTCATCGACAAACC                         GATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG
genomic: GCTCGCCCTACAACAGCAACTCCTCCATGCATCAACCTCATCGACAAACCgtaagatcaa ... taatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcaagcaagaacatcaattgaatctttgttgcttcatctgattaatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACGAGCCAGCAAGCCATGCAGGGACGAAGGCTCAACTACAACTAAATTAAAG
                                          gattaat  putative branch site (score: 3)
                  aattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcaatccatccaccatctcctgcaaatctcgttgcaacttgcaagcaagaacatcaattgaatctttgttgcttcatctgattaatcaccagGATATGGCGATTGAGCACAGCGTAGGGAGGTCGTCGTACGACGCGGACACGAGCCAGCAAGCCATGCAGGGACGAAGGCTCAACTACAACTAAATTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG