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

gtgagtgttcttacgaaattgctctaccaggggtgtttaatttatgccttcaaattgttgaacgatttctgattgctctgtaatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGACGATGACCTGATCGAGTAGATTTGCAATGTGCTACTTTACATCGTCTTG

Basic information

species Oryza sativa
transcript LOC_Os01g42530.1
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|55442436|gb|CV734536.1|CV734536
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|88291555|gb|CI537341.1|CI537341
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|87030406|gb|CI252683.1|CI252683
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|29684837|gb|CB681112.1|CB681112
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCATCAACA                         GCACTAGGCTGAACTGGCAGCGGCTGCACCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|58687745|gb|CK076432.1|CK076432
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|88239222|gb|CI240384.1|CI240384
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGGGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|58589544|gb|CF987852.1|CF987852
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|88263174|gb|CI366948.1|CI366948
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|86511798|gb|CI154431.1|CI154431
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|11564790|gb|AU165426.1|AU165426
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|88906919|gb|CI375991.1|CI375991
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|88283026|gb|CI404472.1|CI404472
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATTTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|125863363|gb|EL586682.1|EL586682
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|3767896|gb|AU031923.1|AU031923
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|88262960|gb|CI366734.1|CI366734
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|29689309|gb|CB685584.1|CB685584
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|86494370|gb|CI137003.1|CI137003
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|12405389|gb|AU166990.1|AU166990
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|88477395|gb|CI414666.1|CI414666
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|88260768|gb|CI363061.1|CI363061
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
EST: gi|14980874|gb|BI305552.1|BI305552
EST:     CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACA                         GCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA
genomic: CCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGA

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), 67 (downstream exon)
Score: 24

CGATGGTAACCTCCACTTTGTGGAAACACCTGCTCTTGCTCCTCCAGATGTCACAATTGATCTAGCAGCCCAGCAACAgtgagtgttc ... taatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGACGATGACCTGATCGAGTAGATTTGCAATGTGCTACTTTACATCGTCTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatttatgccttcaaattgttgaacgatttctgattgctctgtaatgtgcagGCACGAGGCTGAACTGGCAGCGGCTGCAGCCCAACCACTGCCAGATGATGACGATGACCTGATCGAGTAGATTTGCAATGTGCTACTTTACATCGTCTTG
                               ttctgat  putative branch site (score: 24)
             ttcaaatt  TA-rich tract