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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgcagggaatgctaatatagaacctttttaacacataccagacagttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC

Basic information

species Oryza sativa
transcript LOC_Os02g46510.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 12
gtacgtgcagggaatgctaatatagaacctttttaacacataccagacagttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAG--AAAAAAGTCCC
||| |||||   | |  |  | | ||| |||| || ||  |       || |   || ||   | | ||| ||| |||||||| ||||||||||| ||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| |  ||   | | |||    
gtatgtgcaccaagtcttggt-ttgaaactttgtagcatctg------agatggaaaatctcatagtgatacattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCAACAAATCCATACAAGAT--

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------gtacgtgcagggaatgctaatatagaacctttttaacaca--taccagacag----ttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC--
              | |||   ||  |  ||      |  | ||   ||      | | | ||      ||  || || |   |  |   |   |  ||||| ||||||||||||||||||||||| || ||||||||||| ||||| || |  || ||||| || ||||| || || |    || ||  | | ||| |   
tcttttatgtgatttgcgttttggttaatctgtctctggtctttcaaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAA--ACACAGTTCAGG

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 12
gtacgtgcagggaatgctaatatagaacctttttaacacataccagacagttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC
||| ||     |||  ||| |  ||||      |  || ||       |   |||   |||   | |    | |  | ||||| |||||||||||||| ||||| |||||||||||||| ||||| || || |  || || |||||||| || ||||| ||| | ||   ||   ||    
gtatgtatgctgaa--ctagt-cagaatgcccatgcca-atgtttttgaaagcagc-ttcacccttaccaactttctacagGTCTGGGAGAAGAGCGGGTACAATACCGTTGAGTGGGTGCGCTATATTACCAAAGCCGGTTCATATGAAATTAGGTGCTAGAGTTGTGAAATGCAGGTGT

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 11
---------------gtacgtgcagggaatgctaa-tatagaacctttttaacacataccag--acagttcagaactcatgttga-gatgcatatt----ccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC---
                | | | |  |   |||||| | |  ||   | |    | ||||     ||||   |   ||||  |||  |||   || |    | |||| |||||||| || ||||||| ||| ||||| ||||| |||||||||||||| || || ||||| || ||  |||| ||   ||   ||| |    |||   
gtccgttctctacccctgcct-ctcgatgtgctaagttttcaatggtatgtgtagatacggtccacagggaattgctcaccttggtgatatttaatttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACAAGAGCCGGTTCATACGAAATTCGGTGCTA---ATTTGGAACATTTGCCCATG

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------gtacgtgcagggaatgctaatatagaacctttttaacacatac-cagacag---ttcagaa--------ctcatgttg--agatgcatat---tccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC
            | |||    | |||        | | | |   |    || |  ||||| |   ||   ||        ||||||||   || ||| |||   | ||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||||||||||| || || ||||| ||  |||| |                     
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 12
gtacgtgcagggaatgctaatatagaacctttttaacacataccagacagttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGA----TGAAGAAAAAAGTCCC
                    ||   || ||  |    |  |       | ||| | | | || |     ||  |  || |||||||||| ||||| || |||| ||| || || ||||| |||||||||||||| |||||||| || || |||||||| ||   |    ||| | ||        
-------------------gtaagcaaactcgtcgcgat-tgtttaggaattctggaatgatttctttctggctcctc-agGTGTGGGAAAAGAGTGGATACAGCACAGTGGAATGGGTACGCTACATCACAAGAGCTGGATCGTACGAAATAAGGTGCTAAAAAAACGTGAGGGAAGGGA----

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|88967297|gb|CI002489.1|CI002489
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|3766544|gb|AU030654.1|AU030654
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|38480550|gb|CF964639.1|CF964639
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|89162572|gb|CI099264.1|CI099264
EST:     TCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: TCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|86842129|gb|CI338475.1|CI338475
EST:     GTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|88263859|gb|CI367633.1|CI367633
EST:     TCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: TCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|33811255|gb|CF331517.1|CF331517
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACGACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|88284373|gb|CI405819.1|CI405819
EST:     ACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCCTTGAGTGGGTTCGCTACATCACA
genomic: ACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|88543415|gb|CI473419.1|CI473419
EST:     TATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACC-TTGAGTNGGGTTCGCTACATCAC
genomic: TATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGT-GGGTTCGCTACATCAC
EST: gi|3764146|gb|AU030646.1|AU030646
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|86893924|gb|CI314917.1|CI314917
EST:     GTTCCTATGTTTACTGCTTCT-GGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCCTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|86434006|gb|CI094349.1|CI094349
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|109712284|gb|CI104892.1|CI104892
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|3766617|gb|AU030727.1|AU030727
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|3766546|gb|AU030656.1|AU030656
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|88219355|gb|CI218915.1|CI218915
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
EST: gi|3768030|gb|AU032057.1|AU032057
EST:     GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAG                         GTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 45 (upstream exon), 74 (downstream exon)
Score: 43

GTTCCTATGTTTACTGCTTCTGGGTTACGAGTTCGGTTCCTTAAGgtacgtgcag ... catattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttttaacacataccagacagttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC
    ttttaac  putative branch site (score: 43)
     tttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgcagggaatgctaatatagaacctttttaacacataccagacagttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA