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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG

Basic information

species Oryza sativa
transcript LOC_Os02g02410.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 7
gtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgat-atctgttggttaaact-tgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
         ||    |       |  |   ||  |  |||||   | ||||||||| |     | ||       || |||| ||||||||||| |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||||||||||||||||||
--------gtgcgttgctgctgctcatctttttgttgaatggccgattgaatccagtgttgtctgatgaacgaattgaactgtgcagGGGCACACCCCAGATCGAGGTGACCTTCGAGGTGGACGCCAACGGTATCCTGAACGTGAAGGCGGAGGACAAGGGCACGGGCAAGTCGGAGAAGATCACG

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 7
------gtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
         | |    |||| || | ||||  |  ||   |   ||| ||  | ||||   |   |   | |    || | ||   ||||||||||| |||||||| ||||||||||||||||||||||||||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||||||
gtgagcagctaccggagtccggagataaattattactctttttgatgaatggacgaat---gaatccagtgttgtctgatgaactgtgcagGGGCACACCCCAGATCGAGGTGACCTTCGAGGTGGACGCCAACGGTATCCTAAACGTGAAGGCGGAGGACAAGGGCACGGGCAAGTCGGAGAAGATCACG

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 7
gtttgct-catgtccagaaaaaaatgttagcttactcaaa------tggataaatgaatccagcgc-ctgatatct-gttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
||||  | | ||    ||  |    ||   ||  |||||           | ||||  |  |   |  || ||| |  || | |||     |||||| ||||| || ||||| ||||||||||| || || ||||||||||| || || |||||||| || ||||||||||| || || || || |||||||| 
gtttattacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACCCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 7
---gtttgctcatgtccagaaaaaaatgttagct--------tactcaa---atggata--aatgaatccagcgcctgatatctgtt-ggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
     || |    ||  |  |   | |||   ||        | ||| |   ||  ||   | | ||| ||  |   |   | | || || |||     |||||||||||| || ||||| ||||||||||| || || ||||||||||| || || |||||||| || |||||||| || || || || || |||||||| 
gtttgttacctgcgttgatgatgcagtgtcctctctcattattgctccatatattaatgttagtaaattcattggtggtattatatttgggtaattgaacagGGGCACCCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGAACTGGTAAATCAGAAAAGATCACC

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
gtttgct-catgtccagaaaaaaatgttagcttactcaaa------tggataaatgaatccagcgc-ctgatatct-gttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
||||| | | ||    ||  |    ||   ||  |||||           | ||||  |  |   |  || ||| |  || | |||     |||||| || || || ||||| ||||||||||| || || ||||||||||| || || |||||||| || ||||||||||| || || || || |||||||| 
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 7
----gtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaat-ccagcgcctgat--atctgttg-gttaaacttg--cagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
    |||||||  | ||  || |  | |||   || ||  |  | | | |||  ||    |   || ||   | ||||  |||  | |||  |||||| ||||| || ||||| ||||||||||| || || || || ||||| || || |||||||| || ||||||||||| || || || || ||||| || 
gtttgtttgctgctttcatgatactagtgtcctct-acagatgttgttcaattgatgtttgtaactcattggtatgttatgttgtaattgaacagGGGTACCCCTCAAATTGAAGTGACCTTCGAAGTTGATGCAAATGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATAACA

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 7
-------------gtttgctc-atgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
             ||   ||| |  ||      |||||  |  | ||||  |      || |||    |    |||||  || |  ||| |||    ||||| ||||| || ||||| || || || || || ||||| || || ||||| || || |||||||||||||||||||| || || || ||||||||||| 
gtttgcgaaacctgtccactccaactcttctgtaaaatact--cctactgtaggcagaaattgatgtgataatctgattcctat--gttgaac----agGGGAACCCCACAAATTGAAGTCACGTTTGAAGTTGACGCAAATGGTATCCTAAATGTCAAGGCTGAGGACAAGGGCACGGGTAAATCAGAGAAGATCACC

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EDP06859 (Chlamydomonas reinhardtii), 3'ss of exon 7
-gtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcagGGGCACCCCC-CAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGG-----CTGAGG-ACAAGGGCACCG---GCAAGTCGGAGAAGATCACG----
 |   || | |  || |   |  | | |  | ||| |   |  |   |      |  |     |   |  |       | |   | |  |    || |||    |||  |||  | ||  |||    | |  ||||     || |||||     |||||  |  | | ||  |   ||| |  | || |      |    
ggcacgcacctccccggcccatcacgatttcatacacccttccacttaccccaacttcattccaaccccatcaaccccattctgacgcccgtttccacagGACAAGGGCACCGGCAAGAAGGAGAAGATCACCATCACCGCCGAGAAGGGTCGCCTGAGCCAGGACGACATTGAGCGCATGGTGAAGGAAGCTGAGGAGT

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 7
gtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
                        || || |  |||  |  |  || | ||   | ||    || ||| ||        |||||| |||  ||| || || || || ||||| ||| | || ||||| || ||||| ||||| |  || ||||||||||||||||||||||| ||||||||||| 
------------------------gtaagat--ctcccacaggcaactcaacttaacg----atctctctt-------tttgcagTGGCGTCCCTCAAATCGAAGTTACCTTTGAGATCGATGCCAATGGTATCCTCAACGTCAGAGCCGAGGACAAGGGCACCGGCAAGTCCGAGAAGATCACC

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 7
gtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
                   || || | |   |  | | |   | |    | || |       || ||| ||        |||||| |||  ||| || || || || ||||| ||| | || ||||| || ||||| ||||| |  || ||||||||||||||||||||||| ||||||||||| 
-----------------gtaagatctcaagctgtttatacc-acaggcaactcaacttaacaatctctctt-------tttgcagTGGCGTCCCTCAAATCGAAGTTACCTTTGAGATCGATGCCAATGGTATCCTCAACGTCAGAGCCGAGGACAAGGGCACCGGCAAGTCCGAGAAGATCACC

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|58605366|gb|CK033399.1|CK033399
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTCTCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGGATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|29655799|gb|CB652074.1|CB652074
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|428460|gb|D24610.1|D24610
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|58661511|gb|CK050191.1|CK050191
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|55411112|gb|CV723488.1|CV723488
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|5004223|gb|AU069372.1|AU069372
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|29660696|gb|CB656971.1|CB656971
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT

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: 74 (upstream exon), 74 (downstream exon)
Score: 222

GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG
            ataaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA