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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagttaggatatccttatcatttaagtgtgtatatctacttacagatatagagaccatatttctctatccatcgtgtaattgtaagaatgatctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGTCGATGGCTTCTTGGTTACTATGGACATGGTGTTCAGGTGCGAAGACGAG

Basic information

species Oryza sativa
transcript LOC_Os12g36490.1
intron # 1
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|86904002|gb|CI304436.1|CI304436
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88423855|gb|CI609886.1|CI609886
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88395222|gb|CI609538.1|CI609538
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|2309835|gb|C25990.1|C25990
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|86901471|gb|CI308452.1|CI308452
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|86890515|gb|CI303874.1|CI303874
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88359218|gb|CI617883.1|CI617883
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGGTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|86890517|gb|CI303875.1|CI303875
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88394657|gb|CI622531.1|CI622531
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88744683|gb|CI768043.1|CI768043
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|86902423|gb|CI304242.1|CI304242
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88359655|gb|CI622345.1|CI622345
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88351118|gb|CI623340.1|CI623340
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88732142|gb|CI756990.1|CI756990
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|88363938|gb|CI607248.1|CI607248
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGT-CGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAAT-CAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
EST: gi|86888499|gb|CI303781.1|CI303781
EST:     AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGG                         GGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT
genomic: AAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGT

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: 21 (upstream exon), 55 (downstream exon)
Score: 1

GTTTATGGACCACCGTTGTTCTTCTTGGTGGCTTCGTCTCTATGCTTGAGAAGAAGGATTTCTGGAGTCTCACCATCATCACACTCGTCCAAACAGCAGGgttagactgc ... atctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGTCGATGGCTTCTTGGTTACTATGGACATGGTGTTCAGGTGCGAAGACGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatagagaccatatttctctatccatcgtgtaattgtaagaatgatctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGTCGATGGCTTCTTGGTTACTATGGACATGGTGTTCAGGTGCGAAGACGAG
                               taattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagttaggatatccttatcatttaagtgtgtatatctacttacagatatagagaccatatttctctatccatcgtgtaattgtaagaatgatctaaacagGGTGTTCGATGTTCTCCTGAACGAAAAGCTGCGCCATGCTGTGAATTCAGTCGATGGCTTCTTGGTTACTATGGACATGGTGTTCAGGTGCGAAGACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA