Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGAAGATCCCTTCAAAGCTCGGTTATGGTGCTCAAGGGTCACCGCCGACCAT

Basic information

species Oryza sativa
transcript LOC_Os09g32526.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32526.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G115757_T02 (Zea mays), 3'ss of exon 4
gtaatagtaatggtcccaatcaatagctagcta-ctcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGAAGATCCCTTCAAAGCTCGGTTATGGTGCTCAAGGGTCACCGCCGACCAT
                       |   ||  |  |   | || | || || ||| ||    |    ||| | |  |||||       |||| |  ||     | | |||| |||||||||||  | ||||| ||||||||||| || ||| ||||| |||||||||| |||||||| || |||||  ||||||| || || || || ||
----------------------gtgattaattggcatgtctactctttgtgttggttgtgtt----atgtttctctgtctg------aattcctttatctactctatagGATGGGATCAGGGTCTCCTGGGAATGTGCGTTGGTGAAAAGCGGAAGTTGAAGATCCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTAT

upper sequence: LOC_Os09g32526.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ33487 (Selaginella moellendorffii), 3'ss of exon 3
gtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaattt-caatactcc-atttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGAAGATCCCTTCAAAGCTCGGTTATGGTGCTCAAGGGTCACCGCCGACCAT
                                                           | |||   | |   || |  | ||   || ||  | ||||   || |  ||| |||||||| ||  |||| || |||||||| ||||||||||| ||||| |||||||| || |||||||||||||| | ||||||   ||| || |  ||
--------------------------------------------------------gtgagttcttagttttgttctaaagcttggaacttatattactttgatgtcaagGCTGGGATCAAGGGCTTCTAGGAATGTGCGTCGGCGAGAAGAGAAAGCTTAAGATCCCCTCCAAGCTCGGTTATGGGGATCAAGGACAACCACCAAAGAT

upper sequence: LOC_Os09g32526.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ27172 (Selaginella moellendorffii), 3'ss of exon 3
gtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaata--ctccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGAAGATCCCTTCAAAGCTCGGTTATGGTGCTCAAGGGTCACCGCCGACCAT
                                                          || |||   | |   || |  | ||   || ||  ||    | ||| |  ||| |||||||| ||  |||| || |||||||| ||||||||||| ||||| |||||||| || |||||||||||||| | ||||||   ||| || |  ||
--------------------------------------------------------gtaagttcttagttttgttctgaagcttggaacttatattgctttcatgtcaagGCTGGGATCAAGGGCTTCTAGGAATGTGCGTCGGCGAGAAGAGAAAGCTTAAGATCCCCTCCAAGCTCGGTTATGGGGATCAAGGACAACCACCAAAGAT

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|88694794|gb|CI738832.1|CI738832
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
EST: gi|88376918|gb|CI639243.1|CI639243
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88733695|gb|CI756872.1|CI756872
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGA
EST: gi|163925746|gb|EG714582.1|EG714582
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|55432912|gb|CV729479.1|CV729479
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88515169|gb|CI442823.1|CI442823
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88827078|gb|CI777643.1|CI777643
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|5004128|gb|AU069277.1|AU069277
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|33687579|gb|CF315818.1|CF315818
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|66928292|gb|CX115140.1|CX115140
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|218484090|gb|FG956007.1|FG956007
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|163927898|gb|EG713510.1|EG713510
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|58678099|gb|CK066786.1|CK066786
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88375448|gb|CI681220.1|CI681220
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGC-ATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
EST: gi|88739216|gb|CI762724.1|CI762724
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
EST: gi|58676104|gb|CK064791.1|CK064791
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTAGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|86509969|gb|CI152602.1|CI152602
EST:     TTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: TTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|86903638|gb|CI300492.1|CI300492
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGNCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|38480031|gb|CF964120.1|CF964120
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|33686364|gb|CF314603.1|CF314603
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88347332|gb|CI632617.1|CI632617
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|89168554|gb|CI038908.1|CI038908
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88574137|gb|CI665906.1|CI665906
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|218491364|gb|FG953091.1|FG953091
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|163920086|gb|EG709856.1|EG709856
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|2799478|gb|AA752467.1|AA752467
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88576196|gb|CI670341.1|CI670341
EST:     AAGAGGTGACCCAATCGAATTTGAGTCGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCAT-CTTGGGCATGTGCGTNGGCGAGAAGAGGAAGCTG
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCT-GGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
EST: gi|88332240|gb|CI643657.1|CI643657
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTNGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|10794952|gb|AU108918.1|AU108918
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGAAGATCCCTTCAAAGCTCGGTTATGGTGCTCAAGGGTCACCGCCGACCAT
                          atctaaa  putative branch site (score: 3)
                                           ctccattt  putative PPT
                         tatctaaaaatttcaa  TA-rich tract