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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtaccagtgacctatcttagttaatctattgtttatttaaatttgtgatgtaatgcattgtccttcaaatgtttacttttgtaattcaatgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCGTACTCCCGGTCTATAGTTGGTGCTACCCTTGAAGTCATCCAGAAGAAGA

Basic information

species Oryza sativa
transcript LOC_Os07g12250.1
intron # 4
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|88581534|gb|CI698528.1|CI698528
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88348866|gb|CI653910.1|CI653910
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88472849|gb|CI410120.1|CI410120
EST:     ACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: ACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|86522472|gb|CI162678.1|CI162678
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|33670740|gb|CF298979.1|CF298979
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|109711943|gb|CI029113.1|CI029113
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88381633|gb|CI682300.1|CI682300
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|15853700|gb|BI806496.1|BI806496
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88348364|gb|CI639023.1|CI639023
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88388417|gb|CI683189.1|CI683189
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88592045|gb|CI710122.1|CI710122
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88571275|gb|CI662648.1|CI662648
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|218483042|gb|FG956499.1|FG956499
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|86898740|gb|CI296058.1|CI296058
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|3767629|gb|AU031656.1|AU031656
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|55441469|gb|CV734055.1|CV734055
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|55435894|gb|CV731084.1|CV731084
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88514452|gb|CI441958.1|CI441958
EST:     ATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: ATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88763039|gb|CI772595.1|CI772595
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|163927854|gb|EG713502.1|EG713502
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|112787065|gb|EE591987.1|EE591987
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88290337|gb|CI665126.1|CI665126
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88739146|gb|CI762654.1|CI762654
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
EST: gi|88574546|gb|CI666315.1|CI666315
EST:     AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAG                         GATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG
genomic: AGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCG

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: 72 (upstream exon), 74 (downstream exon)
Score: 52

GTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTGAAGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGAAGgtatgagtga ... tgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCGTACTCCCGGTCTATAGTTGGTGCTACCCTTGAAGTCATCCAGAAGAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgtaatgcattgtccttcaaatgtttacttttgtaattcaatgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCGTACTCCCGGTCTATAGTTGGTGCTACCCTTGAAGTCATCCAGAAGAAGA
                           tttacttttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaccagtgacctatcttagttaatctattgtttatttaaatttgtgatgtaatgcattgtccttcaaatgtttacttttgtaattcaatgttttacagGATATTCACGCCGAGGCAGTCAAGAAGAGGCGCCGCACCACCAAGAAACCGTACTCCCGGTCTATAGTTGGTGCTACCCTTGAAGTCATCCAGAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - tgtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - -taatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttttgt