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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatatgtgtatcttcagttagatctgtcctgtaagatataccttttatctattatgaagtgttatagtgttagatatgattctatccatactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG

Basic information

species Oryza sativa
transcript LOC_Os11g24540.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G082330_T01 (Zea mays), 3'ss of exon 10
ttgatatgtgtatcttcagttagatctgtcc-tgtaagatataccttttatctattatgaagtg-ttatagtgttagatatgattctatccatactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
    ||  | ||     |  | || | | |    |  | | |||||| || | |||  |   || ||||  |    |   | || || |  | | | | ||||||||||||||||||||| |||||||| ||||||| |||||| |||| ||||| || |||||||||||||||||||| ||||| ||||||||||||||||
--attacatatacagggaacttgaccagccaacatttgctttaccttctacccattgagtcctgattattcttgctgtattcatgctttggaaattactcagGTTGCTCGTGGTGATAACACTGGGGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG

upper sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 9
ttgatatgtgtatcttcagttagatctgtcctgtaagatatac-cttttatctattatgaagtgttatagtgttagatatgattctatccatactgcac-agGTTGCTCGTGGTGATAACTC---TGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
 || |||   ||| |  |  ||  | | |  | |   ||   | ||  |   | |||| |    | | |  ||    | |  || |     | ||   | |||||||||||||||| ||  |   ||| ||||||||||| ||||| || ||| | |||||| | | |||||| |||||||||||||| ||||| || ||||   
-tgctataaatatttagatatacgttttttgtttttcattctcactcctgagttttattatac-tgaaaaggtctcctgtagttatgagtttccttttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG---

upper sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G44490.1 (Glycine max), 3'ss of exon 10
-ttgatatgtgtatcttcagttagatctgtcctgtaagatataccttttatctattatga-agtgttatagtgttagatatgattctatccatactgcacagGTTGCTCGTGGTGATAACTC---TGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
 ||| |||   ||| |  |  ||  | | || | |    | |  ||  |     |||| | | ||  |  ||||    |    || |     | ||    |||||||||||||||| ||  |   ||| ||||||||||| ||||| || ||| | |||||| | | |||||| |||||||||||||| ||||| || ||||   
cttgctataaatatttagatatacgtttttctttttcattctcactcctgagatttattacactgaaaaggtgtc--ctgaagttatgagtttcctttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG---

upper sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G47600.2 (Glycine max), 3'ss of exon 9
-ttgatatgtgtatcttcagttagatctgtcctgtaagatataccttttatctattatgaagtgttatagtgttag-atatgattctatc--catactgcacagGTTGCTCGTGGTGATAACTCTGG---GGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
  ||   | ||| | |||  | |      |    ||| |   |      |  | |  |    | ||||||| ||   |||   ||  ||   | | ||    |||||||||| ||||| ||  ||||    ||||||||||| ||||| || ||| | |||||| | |||||||| ||||| || ||||||||||| || ||||   
aatggattctgtgttttctataatgctgctttattaaaaaggaagagagaattctggt----ttttatagttttttcatactcttacatgggctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGAGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG---

upper sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA18G53880.1 (Glycine max), 3'ss of exon 9
ttgatatgtgtatcttcagttag-atctgtcctgtaagatataccttttatctattatgaagtgttatagtgtta-gatatgattctatc--catactgcacagGTTGCTCGTGGTGATAACTCTGG---GGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
        || ||  |  ||||  || |||| | ||  | | |          ||| ||   | ||||||| ||  ||||   ||  ||   | | ||    |||||||||| ||||| ||  ||||   |||||||||||| ||||| || ||| | |||||| | |||||||| ||||| || ||||||||||| || ||||   
---tctaatggattctgtgttaacatgtgtctt-tattaaaaaggaagagagaattctggttttttatagttttgtgatactcttacatgggctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG---

upper sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
ttgatatgtgtatcttcagttag--atctgtcctgtaagatataccttttatctattatgaagtgttatagtgttagata-tgattcta---tccatactgcacagGTTGCTCGTGGTGATAACT---CTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
      |   || |||    |||   ||  |  ||  |  |      || |        ||   | |       || ||  | |||  |   ||| | ||    ||||||| |  || || | |    |||||||  | |||||||||||  |||| || ||||| ||||||||||| |||||||| ||||||||||| || ||||   
------tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattcttatttgaaactcccttctttgtagGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG---

upper sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
-----ttgatatgtgtatcttcagttagatctgtcctgtaagatataccttttatctattatgaagtgttatagtgttagatatgattctatccatactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCA---ATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
     || | |  | ||  |||||   ||     |||  |   |     |     | ||||   |   || | || | || | |   |   |   | ||| | |||||||||||||||| |||  ||| | || |   ||||| ||||| || ||| | ||||||||||||||||| |||||||| ||||| ||||| |||||||   
ttctattaacacctataaattcagaatgac--aacctaaatatttagattcaccacaattagacaaatttctggtatgagttct--cttcttttgtgctg-atagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG---

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|2310019|gb|C26174.1|C26174
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|38474789|gb|CF958922.1|CF958922
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|58691853|gb|CK080540.1|CK080540
EST:     TGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCCATTCCGATGCTCTTAAGAATA
genomic: TGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|286796|gb|D15603.1|D15603
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGAA                         GTTGCTCGTGGTGATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATA
EST: gi|58591329|gb|CF989637.1|CF989637
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29664759|gb|CB661034.1|CB661034
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|25799734|gb|CA755695.1|CA755695
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29667214|gb|CB663489.1|CB663489
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29641729|gb|CB646736.1|CB646736
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|218478582|gb|FG949084.1|FG949084
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|396941284|gb|HO188493.1|HO188493
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|27578188|gb|CB000883.1|CB000883
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29633639|gb|CB638648.1|CB638648
EST:     ATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: ATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|29677381|gb|CB673656.1|CB673656
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|86426221|gb|CI071318.1|CI071318
EST:     TATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|218501626|gb|FG955998.1|FG955998
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
EST: gi|218504564|gb|FG954781.1|FG954781
EST:     TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCA                         GTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA
genomic: TCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATA

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: 75 (upstream exon), 70 (downstream exon)
Score: 57

GTTGCATCAGCTCTTCTTAGTGCTGCATTTGTGTATGATGTTTTCTGGGTGTTCATTTCACCTCTTATATTCCATGAAAGTGTCATGATTGCAgtaagtgcat ... tactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctattatgaagtgttatagtgttagatatgattctatccatactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG
      tattatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatatgtgtatcttcagttagatctgtcctgtaagatataccttttatctattatgaagtgttatagtgttagatatgattctatccatactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCAATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG

- - - -gtgtatc
- - - - - - - - - - - - - tgtcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattct