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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG

Basic information

species Oryza sativa
transcript LOC_Os11g06390.6
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 2
gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
||| || || ||  ||| |  |  | |||  ||     |    || | ||    | ||||||||  |        ||||||| | || |  ||||||||||| |||||||| ||||||||||| |||||||||||||| || || || || |||||||||||||| |||||||||||||| ||||||||||||||||
gtttgtagttcttgttcatgctggtacttcatatt--ctgcaacctttttctgctaatttaatcacacg------ttttcttacaaactattggcagGCTGGTTTTGCTGGTGACGATGCGCCAAGGGCTGTTTTCCCAAGCATTGTCGGACGCCCCCGTCACACTGGTGTGATGGTTGGCATGGGGCAGAAGGATG

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 2
gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
              || |||||  || ||            |  |||||| |      ||  ||   || |||| |    |  | || | |||||||||||| |||||||| ||||||||||| |||||||||||||| || || || || ||||| |||||||| || ||||||||||| ||||||||||||||||
-------------gtttgtagttcttgttcacgctg-----cttcatgttcagtaacattgttctgttaatttaatcacatcacaaactactggcagGCTGGTTTTGCTGGTGACGATGCGCCAAGGGCTGTTTTCCCAAGCATTGTTGGACGCCCACGTCACACTGGCGTGATGGTTGGCATGGGGCAGAAGGATG

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 1
gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtata-ctttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
     | || || |   |   | ||| |||||  ||  |         | |    |  || |    ||| ||  |  |||  |   |||      |||||||| |||||||| || ||||| ||||||||||| || || ||||| || || || || || ||||| ||||| |||||||| ||||| || |||||||
---gttagtacttagcggctttgttt-tttgtttcatgtgcttgtgcatctgctagccttgagttcataactgaatctttgattttaatatggaacagGCTGGATTTGCTGGTGATGATGCTCCCAGGGCTGTCTTTCCCAGTATTGTTGGCCGACCTCGACACACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 1
gttcgtggtgctcattcgtagtatttctt-tgtagcagttatccccatgt-ttatgtgatttaatcgtatact--ttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
 | | |    ||    ||| |    |    ||   |        |   |  || |  ||   || |  || ||    |    | |  ||   ||   ||||||||| |||||||| || ||||| ||  | ||||| |||||    |||||||| || ||||| ||||||||||||||||| || ||||| ||||||    
-tccatttaacttgggcgttgggcctggcgtgggccccgcgctgcagcgcgttgttcgagcaaacctgatgctggcgatcgctgtgtcgccgtgtccgcagGCTGGCTTTGCTGGTGATGATGCCCCTCGCGCTGTGTTCCCCTCCATCGTGGGCCGGCCCCGCCACACCGGTGTGATGGTCGGGATGGGCCAGAAG----

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 1
---gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttct-tgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
      |   ||||    |    | ||    |   |||  ||     ||| ||  |||    ||||   |  |       ||   |   |||||| | |||||||| || ||  | |||||||| ||| ||||||||||||| || ||||||||||| ||  | |||||||| |||||||| || ||||| ||||| || |
gcatagcactgtgcattataaaggcatgaaatcccagcttttgatggcattttattgttgaataattccaggcgccggaattgaatttcaattgccg-cagGCTGGTTTCGCCAGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
--gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttactt--ttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
   ||     |  | |||  || |         | | |  ||  |  || | |     ||    ||| | ||| |  ||  || | | ||||||   ||||||||| || ||||| |||||||| ||| | ||||||||||| || || || ||||||||| | ||||| || |||||||| |||||||| |||||||| |
ctcttttgcatctttatttataatgggcagacattggatgtagactaatttatgatcaatcctctcgaa-actgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
--gttcgtggtgct----cattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttactt--ttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
   ||| || |       | ||| |  || | || |  |  ||| |   |     || ||   |  |     | ||  |  ||  || | | ||||||   ||||||||| || ||||| |||||||| ||| | ||||||||||| || || || ||||||||| | ||||| || |||||||| |||||||| |||||||| |
caattcatgctataatggcgttcatgataatactattca--agtgacttcag---ttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------gttcgtggt--gctcattcgtagtatt-tctttgtagcagttatccccatgtt-tatgtgatttaatcgtatactttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
                                                                                  || | | ||  | ||| || ||||| | | |   || | ||  ||  |||  |       || | |   ||    |   || | | |||         |||||||| || || || |||||||| ||| ||||||||||||| || ||||||||||| ||  | |||||||| |||||||| || ||||| ||||| || |
gtatgcatgcttaccgcatatacgactgtaattctcccatgcaaatcgagcatgctaacaatcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcg---------cagGCTGGTTTCGCCGGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
                                        | | | |  |   | | |||  | ||  | |||  |      |     | || ||||||||| ||||| || |||||||| |||||||| || || || || || ||||| || |||   ||||| || || |||||||| ||||||||||||||||
---------------------------------------gtgcgc-tcctggcgcggtttc-ttgtggattttgatccggggggtgtgttcttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
                                        | | | |  |   | |||||  | ||  | |||  |      |     |  | ||||||||| ||||| || |||||||| |||||||| || || || || || ||||| || |||   ||||| || || |||||||| ||||||||||||||||
---------------------------------------gtgcgc-tcctggcgcgatttc-ttgtggattttgatccggggggtgtgtttttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

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|58669469|gb|CK058155.1|CK058155
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|58659094|gb|CK047774.1|CK047774
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|218491871|gb|FG949270.1|FG949270
EST:     CAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
genomic: CAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|58601398|gb|CK011926.1|CK011926
EST:     CGAGGACATCCAGCCCCTTGTGTTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCANGGCTGTTTTCCCTAGTATCGTG
genomic: CGAGGACATCCAGCCCCTTGTG-TGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|58690729|gb|CK079416.1|CK079416
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGTGCTGTTTTCCCCTAGTATCGT
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTT-CCCTAGTATCGT
EST: gi|58607922|gb|CK035955.1|CK035955
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGTGCTGTTTTCCCTAGTGTCGTG
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|29643809|gb|CB648816.1|CB648816
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG
              atttaat  putative branch site (score: 4)
      tttatgtgatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTGGGGCGCCCCCGTCACACCGGTGTGATGGTTGGTATGGGGCAGAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG