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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggattcattccttgtcaagtatcttgttagtaaagcacatcataaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG

Basic information

species Oryza sativa
transcript LOC_Os02g17320.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
ggattcattccttgtcaagtatcttgttagtaaagcacatcataaatttttgaat-----agaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
   ||||| |  |   |   |  |  | |  | | ||  | || |        ||     |  || |  || || ||  ||| |||| || ||||| || |||||||| || || ||||||||||| || || |||||||| ||||||||||| ||||||||||||||||||||  ||||||||||||||||  |||||
---ttcatgcactagaattcaattcatcacaagaacatgt-atgatcccccctatccttgaataaagtgta-ctctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 10
ggattcattccttgtcaagtatcttgttagtaaagcaca--tcataaatttttgaatagaaaggcata-actatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
     ||| |    |  |          | || |   ||  |||| | |  |   |   | |   ||  ||| |   ||| |||| || |||||  | |||||||| || ||||||||||||||| | || |||||||| ||||||||||| ||||||||||||||||||||  ||||||| ||||||||  |||||
---aacatgcacaattgacccctcatgcactagaattcaattcatcagtcatcacaagaacatctatgtactctacaaatgatttgctacaactggtttccagTGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
ggattcattccttgtcaagtatcttgttagtaaagcac-atca-taaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
   ||| |||||  | |      ||  |    |   |  |||| |  | ||||  ||| | ||   |       |||| | |  | |||||  |   | |||||| ||||||||||| |||||  | || ||||||||||||||||| || |||||||| ||||||||||| || ||||| ||||||||  |||||
ttcttctttcctaattactcggtttaatgtggacctatgatcactgcaattttatataaatagaatttgtcc--ttaaatttgatatgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
-------------------------------------ggattcattccttgtcaagtatcttgttagtaaagcac-atca-taaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
                                        ||| |||||  | |   |  ||| |   ||   |  |||| |  | ||||  ||| | ||   |       |||| | |  | |||||  |   | |||||| ||||||||||| ||||| || || ||||||||||||||||| || |||||||| |||||                               
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCC--TTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
ggattcattccttgtcaagtatcttgt-tagtaaagcacatcataaatttttgaatagaaaggcata----actatgttaattat----tttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG-
         ||||   ||   |  ||| ||     |||    |||| || |||  ||||||  |||     | |||  ||||||     ||  |  |   |   | |||||| ||||||||||||||||| ||| | |||||||| |||||||| || |||||||| ||| | |||||||| ||||| ||||||||  | ||| 
---------ccttaagaaaccttgtgtgtatctttgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaattaatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
ggattcattccttgtcaagtatcttgt-tagtaaagcacatcataaatttttgaatagaaaggcata-------actatg-ttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
         || |   ||   |  ||| |      |||  | |||| || |||   |||||  |||        |  ||  ||||| ||||  |  |   ||  | |||||| ||||||||||||||||| ||| | |||||||| ||||||||||| |||||||| ||| | |||||||| ||||| ||||||||  | |||
---------ccctaagaaaccttgtgtgtctctctgcagtttataatttattgttaagaaattcattttctgttatcataattaataatttaatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
ggattcattccttgtcaagtatcttgttagtaaagca--catcataaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
                             |||||| |  || | ||||   |   |   || | ||  ||||| | ||| ||||| |      |      || ||||||||||||||||| ||  |  | |||||||||||||| || ||||||||||||||||| ||||| || ||||| ||||||||  |||||
-----------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatat-aatgattttgtct---ctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
ggattcattcct-tgtcaagtatcttgttagta----aagcacatcataaatttttga-atagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
   | | ||||| | ||     | | |||  ||    | | || ||   |   ||| | ||   |     | || |  || ||  | || || ||  |    | ||||||||||| ||||||||||| || || ||||| ||||||||||| || || |||||||| || |||||||| ||||| ||||||||  |||||
--gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaa--taatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 11
----ggattcattccttgtcaagtatcttgttagtaaagcacatcataaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
    | |             ||| || ||  | || | | ||    |   | ||||  |      ||||     | | ||  || ||||   |||  |  ||||||||||||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| || |||||||| || || ||  | |||
aaaggaaaaagaagtgcaaaaagcatattcctggttatggacccattttctctttgtcttt---tgcattttggtttgaaccatcttctcttactgatg-ccagTGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------------------------------------------------------ggattcattccttgtcaagtatcttgttagtaaagcacatcataaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
                                                                                                        |  |||     | |  ||||  | | ||    |    |   | | | |   |    || | |    | ||| | ||  |||  |  |   |||||| ||||||||||||||||| |||||||| || ||||| || || || ||||| |||||||| || ||| |||| |||||  | || || |||
gttatcttttatttattgtaccaccgaagtgggatattgttacgagttcactgggcttgtggagtgtcagtagtctggttgcatcttcttatgcagtaatgctgtagctttatttgaagtttgtgtgcagagattgtttcgaggatgtaagtcacagaatatcagtcaactcattctgtta-gcacatgttgcgcagTGGAGAGAGTATGGAGAATGCTTTGCGGGCGTGTTGCAAGGGCATCAAGATTGGAAAGATTCTAATACACCGGGAGGGAGATGACGGGAAGCAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S83_234V6.4 (Physcomitrella patens), 3'ss of exon 11
-----------------ggatt--cattccttgtcaagtatcttgttagtaaagcac-atcataaatttttgaatagaaaggcataacta------tgttaattattttctgcaacttctct---ccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
                 |  ||  ||    |  | | ||   |||   ||   | ||    ||       ||| |  || | ||| || |      || |||||||| |   |   ||||     | || || ||||| |||||||||||| ||||||| ||||||||||| || || ||||| |||||| | || ||  | |||||||| |||||  |||||
gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctga-tctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ31180 (Selaginella moellendorffii), 3'ss of exon 10
ggattcattccttgtcaagtatcttgttagtaaagcacatcataaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
                                         |    ||  ||      | |  ||  |   | | || ||||  ||    || |    || || || ||||||||||| ||  |||| || || ||||| || |||||||| || ||||||||||| ||| ||||||| |||||||| ||||| 
---------------------------------------gtactgtttgctgccattgatgatatttcgtggctgatgatttcgtggcgtttgt----agCGGAGAAAGTATGGAGAACGCTCTGCGTGCCTGTTGCAAGGGAATAAAAATCGGCAAGATTCTTATACACCGGGAAGGCGACAATGGAAAACAA

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ17251 (Selaginella moellendorffii), 3'ss of exon 9
ggattcattccttgtcaagtatcttgttagtaaagcacatcataaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
                                         |    ||  ||      | |  ||  |   | | || ||||  ||    || |    || || ||  |||||||||| ||  |||| || || ||||| || |||||||| || ||||||||||| ||| |||| || |||||||| ||||| 
---------------------------------------gtactgtttgctgccattgatgagatttcgtggctgatgatttcgtggcgtttgt----agCGGGGAACGTATGGAGAACGCTCTGCGTGCCTGTTGCAAGGGAATAAAAATCGGCAAGATTCTTATACACCGGGAGGGCGACAATGGAAAACAA

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|88329947|gb|CI652334.1|CI652334
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
EST: gi|86902718|gb|CI306521.1|CI306521
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTG
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTG
EST: gi|88570524|gb|CI661897.1|CI661897
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
EST: gi|12623049|gb|AU173262.1|AU173262
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGGGTGGTATCTCAGTGATTAGAAG                         TGGGGAGAGTTTGGANAATGCATTGNGGGCATGCTG
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTG
EST: gi|88335863|gb|CI645464.1|CI645464
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
EST: gi|88343858|gb|CI654894.1|CI654894
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
EST: gi|66922909|gb|CX109757.1|CX109757
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAACGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
EST: gi|58687647|gb|CK076334.1|CK076334
EST:     ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG                         TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT
genomic: ACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAGgtagtaactt ... ttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
                         tgttaat  putative branch site (score: 3)
                                            cttctctcc  putative PPT
                  ataactatgttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggattcattccttgtcaagtatcttgttagtaaagcacatcataaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA