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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctcaaccattttacttttaagaataaatctagtgccactttatctctatttgttttggcaagttatgttgacacttcattttttatgctgctg...

Basic information

species Oryza sativa
transcript LOC_Os08g09240.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g09240.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G014975_T01 (Zea mays), 5'ss of exon 2
GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctcaaccattttacttttaagaataaatctagtgccact-ttatctctatttgttttggcaagttatgttgacacttcattttttatgctgctg--------
||||||||||||||||| |||||||||||||| || ||||| ||||| || ||||||||||  |||||||      | |||| ||  || | |||   | ||  || |  | |||||  |   | |  |||  | ||  ||   | | || |||        
GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATCGACAAGAAAAAgtcagttccgaaccatt------tcaagattatttcaattgcatttcttgacttttatggtttttcc---tgacattgcaatttttttccctgtacttctgaaagtagt

upper sequence: LOC_Os08g09240.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G134613_T01 (Zea mays), 5'ss of exon 3
GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctcaaccattttacttttaagaataaatctagtgccactttatctctatttgttttggcaagttatgttgacacttcattttttat-gctgctg-----
||||||||||||||||| |||||||||||||| || ||||||||||| || |||||||   |    |   |  || || ||  |  || |      | ||| ||| |   | |||| | |  |||| ||    ||  | || | |  | |||       
GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatttcacgagtatctctttag--tgcatttg----tattttctctatcagtttttttggacattatattttttctgtacttctaaaagttgccttatac

upper sequence: LOC_Os08g09240.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagt------tctcaaccattttacttttaagaataaatctagtgccactttatctctatttgttttggcaagttatgttgacacttcattttttatgctgctg
|| ||||| ||||||||||| || |||||||| |||||||||||||| ||||||| |||      |||  |   || |  |||  | |   ||  ||||   || |  |   |||   |||  ||   |||| |  | | |||||    | |       
GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaacatctttatttttattttttataaatagaagttagtcaaacatcttgattatc-atttgtgctttttatatccatatttcatgaagtttat-----

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|55434634|gb|CV730441.1|CV730441
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|55436298|gb|CV731287.1|CV731287
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|33659136|gb|CF281749.1|CF281749
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|58590250|gb|CF988558.1|CF988558
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|218487512|gb|FG953689.1|FG953689
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|25802781|gb|CA758742.1|CA758742
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|33657525|gb|CF280139.1|CF280139
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|88721866|gb|CI743378.1|CI743378
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|88974162|gb|CI002783.1|CI002783
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|88428393|gb|CI564861.1|CI564861
EST:     ATTGTTGAGAAGGCTGAGAGGATTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|58695129|gb|CK083816.1|CK083816
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|88963125|gb|CI026798.1|CI026798
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|89168539|gb|CI038893.1|CI038893
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|88833607|gb|CI077088.1|CI077088
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|33671347|gb|CF299586.1|CF299586
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|58593892|gb|CF992200.1|CF992200
EST:     ATTGTTGAGAAGGGGGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|55431390|gb|CV728708.1|CV728708
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|218486561|gb|FG954049.1|FG954049
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATGGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|163926759|gb|EG715047.1|EG715047
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|33682438|gb|CF310677.1|CF310677
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|87012764|gb|CI295208.1|CI295208
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|58586677|gb|CF984985.1|CF984985
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTGGGTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|88424094|gb|CI689796.1|CI689796
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
EST: gi|58599898|gb|CK010426.1|CK010426
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAA                         GTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctc ... ctatatgcagGTACCTTGTTCCCGCTGACCTCACGGTTGGACAGTTTGTGTATGTTGTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctcaaccattttacttttaagaataaatctagtgccactttatctctatttgttttggcaagttatgttgacacttcattttttatgctgctg

- - - - - - - - - GAGAGG
- - - - - - - - -  AGAGGA
- - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - -  AAAGAA