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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT

Basic information

species Oryza sativa
transcript LOC_Os09g07510.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
-ggagcaaatagtgcatgat-tgagccagttgggac-atttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
  |    |||  | || |   | ||  | |||  |  | ||   |  ||  |  | ||   || || |   |   |  ||   |  || |  ||||    |||| |||||||| || ||  | ||||||||||| || ||||||||||||||||| |||||||| || |||||||||| ||||||||| || |||||||||||
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcataca--ttacatcagctaagaagaaactgttttgactctttaac-tcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 3
-ggagcaaatagtgcatgat-tgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
  |  ||  |  |   |  | | |      || |   ||||   |  || | ||| |   |  |||    | || |  || ||  |  |||| |  |  ||||||||||||| || ||  |  | || ||||| || ||||| ||||| ||||||||||||||||| |||||||| || |||||||| ||||| || || ||
atgttcatttgttaagtagtgttattttactgtgttttttaa-gttgatctgctggaag-tgcatacattaactgatgatttttttatccttgttcttgcagATCAAGATTCTGTTCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGGAAATTGTTGGAACCTCAAGATTGCGTGGCACATATTCTTCCTGTCATAGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 3
----------------------ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                              |  ||  |      | || |    |  |  |  ||| || |||   |    || |     |     |||| |  ||             |||||||||| || ||  | |||||||| || || || |||||||||||||||||| || |||| |||||||||||  |  ||||||| || ||         
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaatacaattggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCG--------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 3
----------------------ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                              |  ||  |      | || |    |  |  |  ||| || |||   |    || |     |     |||| |  ||             |||||||||| || ||  | |||||||| || || || |||||||||||||||||| || |||| |||||||||||  |  ||||||| || || ||||||||
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaatacaattggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
-------------------------------ggagcaaatagtgcatgattgagccagttgggacatttac-----tatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattacc-------agATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                               |  | |||  ||   | |||  | | |||   | ||||||     |     |||| |  || ||    |||| |  | ||    ||  |   |  || | | |       |||||||||||| ||  | |||||||| || || ||||||||||||||||| ||  ||||||| |||||||||||||| |||||||| || || ||||||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcattt-gtctgttac-atatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 2
-ggagcaaatagtgcatgat-tgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
  |  ||  |  ||  |  | | |      || |   ||||   |  ||   ||| |   |  |||    | || |   | ||  |  |||| |      |||||||||||| || ||  |  | || ||||| || ||||| ||||| || |||||||||||||| ||||||||||| |||||||| ||||| || || ||
atgttcatttgttgagtagtgttattttactgtgttttttaa-gttgatccgctggaag-tgcatacattaactgatggtttttttatccttgttcctgtagATCAAGATTCTGTTCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGAAAATTGTTGGAACCTCAAGATTGTGTGGCACATATTCTTCCTGTCATAGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
-------------------------------ggagcaaatagtgcatgattga-gccagttggg-----acatttactataca--tgttctgcag-----cctaaataa---tgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                               |  | |||  ||   | |||   | |  |||       |||||   | |     |||  || ||     ||| |||     | | |||   |||||   | |   | |   | ||||||||||||| ||  | |||||||| || || ||||||||||||||||| ||  ||||||| |||||||||||||| |||||||| || || ||||||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------------------------------ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                                                                                                  |  |||   ||  ||||  |     ||||    ||  || | ||         |  | |    ||| | ||    |    ||      ||  |  |||| |||||||| ||  |  | ||||| |||||||| ||||| |||||||| || ||||||||||| || |||||||| ||||  ||  | || ||||||||
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttat-taccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                 ||||| |    || | | |||| |     |  ||| |||| || ||| |   || ||    ||     |  ||||   || ||||||||||||| ||  | || ||||| ||||| || |||||||||||||||||||||||||| || || ||||||||   ||| || ||||| || |||||
---------------gtattgaac--actgag-cgtttatt-----tactctacagcatatata-tttgtcgaatttcatcttacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagccta-aataatgca---tctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
     || |   |||  |||  |   ||    |  |   ||  |     | |  |   || |||| | ||   | |||  || ||  || | ||    || ||||||||||||| ||  | || ||||| ||||| || |||||||||||||||||||||||||| || || || ||||| ||||| || ||||| || |||||
--ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgacatt--gatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 4
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggcct----tttattacca-----gATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
      |||    ||   |||      ||  |   ||  |  ||  | || |  |    || ||    | | |      ||| | || |    ||||||  ||     ||||||||||| ||  | || ||||| ||||| || ||||| ||||| || ||  |||||||||| |||||||||||||||||||| ||||| || |||||
------aatg--acaaagttgtttttctttcgtttttgccggtat-ttttttatattggaagtatgatagccatttgggttgttagcttacaatttattttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAAAGCTGTTGGAACCTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGT

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|300215963|gb|HO088589.1|HO088589
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
EST: gi|58672176|gb|CK060862.1|CK060862
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
EST: gi|300215769|gb|HO088395.1|HO088395
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
EST: gi|29658915|gb|CB655190.1|CB655190
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
EST: gi|313081057|gb|HO213643.1|HO213643
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGT
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGT

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: 73 (upstream exon), 72 (downstream exon)
Score: 164

AGGGCAGCTGCATCAAATCTTGGAAAGTTTGCAGCCACAGTTGAACAGAACTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                       atctaac  putative branch site (score: 164)
                                         ccttttatt  putative PPT
                          taacaatatt  TA-rich tract