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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaaaacctagaaaatgaaacaaaagaatctgtgctttataaatttccattaacattgaagtattgccttcactgactaatgcaaaatttatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTATCATTGGAGATGAATCCTCTATATACGTCACGACTGATTGCTCATCTTG

Basic information

species Oryza sativa
transcript LOC_Os11g03780.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 3
-actaaaacctagaaaatgaaacaaaagaatctgtgctttataaatttccattaacattgaagtattgccttcactgactaatgcaaaatttatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTATCATTGGAGATGAATCCTCTATATACGTCACGACTGATTGCTCATCTTG
 || ||    |      |     ||     | | |   |||||  | |         || || | |     | |||||   ||    ||||  |  || ||| ||||||||||| || ||  |||| |||||||||||||| || ||||| || |||||| ||||||| |  ||| | ||    |||||| |  | |||||
aacaaaggaatgatttgttggttaacttgttgttt-tgttataggtatgtcactgtttttaattttaagtataactgaaatattatgaattcttgttttagGATTTGAAGCTGGCGGTCCTAACACTCCTTCAAATATTGATCCTTGGTCAATTATTGGAAATGAATCATTGATAAATGTTGAAACTGATCGTACCTCTTG

upper sequence: LOC_Os11g03780.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 3
actaaaacctagaaaatgaaacaaaagaatctgtgctttataaatttccattaacattgaagtatt--gccttcactgactaatgcaaaatttatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTATCATTGGAGATGAATCCTCTATATACGTCACGACTGATTGCTCATCTTG
   |||    |  ||||| |  |   |    |   |||  |   |||  |   |       || ||     || | |||   ||    ||||  |  || ||| ||||||||||| || ||  |||| ||||||||||||||||| ||||| || |||||| ||||||| |  ||| |  |    |||||| || | |||||
--caaatgtgaacaaatggatgatttgttgtttaacttgttttgtttttaggtaggccactgtttttaattttaagtgaagtattatgaattcttgttttagGATTTGAAGCTGGTGGCCCTAACACTCCTTCAAATATTGACCCTTGGTCAATTATTGGAAATGAATCATTGATAAATATTGAAACTGATCGCACCTCTTG
















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|88356864|gb|CI619350.1|CI619350
EST:     TAAACATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
EST: gi|58671742|gb|CK060428.1|CK060428
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
EST: gi|88695436|gb|CI737474.1|CI737474
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGC
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGC
EST: gi|88727707|gb|CI749509.1|CI749509
EST:     AACCATGCCGGAGCTGGTGGGATATGGGNCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGGCCCACACCCCTTC
genomic: AACCATGCCGGAGCTGGTGGGATATGGG-CGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTC
EST: gi|88692709|gb|CI736284.1|CI736284
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGAC
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGAC
EST: gi|88718003|gb|CI741513.1|CI741513
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCT
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCT
EST: gi|88719222|gb|CI742732.1|CI742732
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCC
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCC
EST: gi|88726971|gb|CI750626.1|CI750626
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCCTTCAAATATTGACCCATGGTCT
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCC-TTCAAATATTGACCCATGGTCT
EST: gi|58604955|gb|CK032988.1|CK032988
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
EST: gi|88392471|gb|CI612945.1|CI612945
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
EST: gi|88311923|gb|CI577529.1|CI577529
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
EST: gi|88400278|gb|CI590968.1|CI590968
EST:     TAAACATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GATTTGAAGCTGGAGGGCCCCACACCCCTTCAAACTATTGATCCCATGGTC
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAA-TATTGA-CCCATGGTC
EST: gi|88372707|gb|CI612635.1|CI612635
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGG
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGG
EST: gi|88314494|gb|CI604978.1|CI604978
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
EST: gi|88405712|gb|CI609611.1|CI609611
EST:     TAATCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCC
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCC
EST: gi|88695959|gb|CI739534.1|CI739534
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCC
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCC
EST: gi|88314645|gb|CI606713.1|CI606713
EST:     TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG                         GGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA
genomic: TAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAGgtaactgtca ... tatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccattaacattgaagtattgccttcactgactaatgcaaaatttatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTATCATTGGAGATGAATCCTCTATATACGTCACGACTGATTGCTCATCTTG
                              gactaat  putative branch site (score: 2)
                                 taatgcaaaatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaaaacctagaaaatgaaacaaaagaatctgtgctttataaatttccattaacattgaagtattgccttcactgactaatgcaaaatttatacttcagGGTTTGAAGCTGGAGGGCCCCACACCCCTTCAAATATTGACCCATGGTCTATCATTGGAGATGAATCCTCTATATACGTCACGACTGATTGCTCATCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG