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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttaacaaaaaattcatttgggagacacaagtgaaattattagtatactatgggaacatctctacctaacccgcctaactttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA

Basic information

species Oryza sativa
transcript LOC_Os05g51490.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
tttttaacaaaaaattcatttgggagacacaagtgaaattattagtatactatg--ggaacatctctacctaacccgccta------actttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA
             | |    | ||  |    | |  |||| |||  ||  ||||  |  || | |     || |     ||      | || ||   |||     |||||||| || ||| | || |||||||| || || || || ||||| ||||| ||||||||||| |||||||| |||||||| || || | ||| || ||||
--------gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgtattggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA

upper sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
-tttttaacaaaaaattcatttgggagacacaagtgaaattattagtatactatggga-acatctctacctaacccgcctaactttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA
 |  |        |  | |||        ||||   |  ||  | |     |  |    | |    ||  |         || |||  |||||  |   ||||| ||  ||||| | || || || |  ||||||||||| || |||||||||||||||||||| ||||| || |||||||| ||||||   || ||| |||
ataatatgttgggacgttattcatattctacaa--tattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA

upper sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
------------------------------------------------tttttaacaaaa--aattcatttgggagacacaagtgaaat-tattagtatactatgggaacatctctacctaacccgcctaactttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA
                                                |  ||  | |      | ||||  |      | | |  ||| | |||| | | |  ||    |  ||| ||  |     |    ||||  || |      |||||||| || ||| | |||||||| || ||||| || || || |||||||| ||||||||||||||||| || |||||||| || |||   || || || |
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA

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|88728999|gb|CI752509.1|CI752509
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88402355|gb|CI596216.1|CI596216
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88333410|gb|CI642447.1|CI642447
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88571158|gb|CI662531.1|CI662531
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88426371|gb|CI576613.1|CI576613
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88341949|gb|CI644286.1|CI644286
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88338584|gb|CI645838.1|CI645838
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88348978|gb|CI654022.1|CI654022
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88411328|gb|CI564449.1|CI564449
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|58607323|gb|CK035356.1|CK035356
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88358042|gb|CI650778.1|CI650778
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88718021|gb|CI741531.1|CI741531
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|29669887|gb|CB666162.1|CB666162
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88407509|gb|CI586350.1|CI586350
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88390893|gb|CI611119.1|CI611119
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
EST: gi|88407840|gb|CI588869.1|CI588869
EST:     CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCG                         GTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC
genomic: CCGTCGCCGCCATGTTCTGGCGCATGACTGGTCTCTCCGCGGCCTCGCCGgtgagtccct ... tactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactatgggaacatctctacctaacccgcctaactttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA
                             gcctaac  putative branch site (score: 2)
                                taactttgtaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttaacaaaaaattcatttgggagacacaagtgaaattattagtatactatgggaacatctctacctaacccgcctaactttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG