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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG

Basic information

species Oryza sativa
transcript LOC_Os02g08120.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
------ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttct-gtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
       ||||| ||||      | ||    | ||| | | |  |    |||   | | | |    |||| ||  | | |  |  | ||        | | ||||||||||||||||||||| |||||| ||||||||||||||||||| |||||||||||||||||||||||||||||||| 
tggctctcttgcttgtttggcgttttat--tttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctcta-----tctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
ccttgcgtgttcattactgtaa---agctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctc-tgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
 ||||| || |      | ||    | || |  |  | | |   | |   | | | | |    |||| |  |  || |   || |  | || | |  | |||||||||||||||||||| |||||||||||||||||||||||||| ||||||||| |||||||||||||||||||||| 
-cttgcttgcttggcgttttattttaacttatta-ataacagaataatcggtgacctatcacattctat--ttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 2
---ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
     ||  |   | |  |||  | |  | ||  ||| | |   | | |||| |  |   | | | |||  |  ||| |||   |   | |     | |||||||| |||||||||||  | |||||||| ||||||||||  ||||| ||||||||||| || |||||||||||||| 
tgttattagggtattaacacta-atatgttaatctgttaaagcttaatttgc-tgatcaatgcatttgttgtt-tttcttcatttattcataccaatttgcagTGTAATTGTTGAAGCCCTGAAGGTGGACAGTCTGCAGAAACTTTGTTCATCACTGGAGCCTATTCTTCGTAGAGTT

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 1
ccttgcgtgttcattactgtaaagctcaac---atgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcc-tctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
      |   ||| ||  |      | | |   || ||      | || |  |   |   ||  | | |  || |||| | |  ||     | ||  | |||||||| |||||||||||  | ||||| || ||||||||||  |||||||| |||||||| || ||||| || ||||| 
--gaaaggaatcactaaggaggcagttagcttaatttggtgtcttaaacttggctatgaatttgtttat--tgcttttattcatttatttatgttaatttgcagTGTAATTGTTGAAGCCCTGAAGGTTGACAGTCTGCAGAAACTTTGCTCGTCACTGGAGCCTATTCTACGCAGAGTT

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
-----ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
       ||   |  | |||| | || |  ||| |  ||  |    | | ||   | | |||||  | |   || |||  ||  | | | | |  || || ||||||| ||||| |||||  | |||||||| ||| |||||| ||||||||||||  | ||||| |||||||||||||| 
atagggttttatttcttattaat-tataattcatctagtt-gtttctaatttatatttattgttagtttcatataattgatt--gatgcacatacttttc-gcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G06320.1 (Glycine max), 3'ss of exon 1
ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtctt-ttgttcttctgtcatgattttttccgcttcgcctctttc--tctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
   |  |   | ||   | || |  |  |    | |   ||||  ||     |  || |   |||   |   | || |   | | |  | | |   | |||||||| |||||||| ||  | |||||||| ||||||||||  ||||||||||||||||| || ||||| || ||||| 
---taagcagttatgtttctatatgttcaagcttaatttggtgtcttaaacttggttatatatctagtaatttcttatattcattgtttatgttattttgcagTGTAATTGTTGAGGCCCTGAAGGTGGACAGTCTGCAGAAACTTTGCTCATCACTGGAGCCTATTCTACGCAGAGTT

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
--------ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
          ||   | ||  | |   |||   || |  |    |    | | ||   | | |||||  | |   || |||  ||  | | | | | |||   |||||||| ||||| |||||  | |||||||| ||| |||||| ||||||||||||  | ||||| |||||||||||||| 
aaagaagattttatttcttattaatcataa---tccatctacttgtttctaatttatatttattgttagtttcctataattgatt--gatacacatattt---tgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------ccttgcgtgt-tcattactgtaaagctcaacatgtgagaaggtga--attgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
                                                  |||  | | | |||  | |  || |  |    ||| ||   |    ||  || | ||| |  |||||     ||      | |  |  | | |   |||||||| ||||| ||||| || ||| |||||||| | ||||||||||| || ||  ||||||| ||||||||  |||||
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtgg-atttgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
-----ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
     |||||| ||||   ||   |||| ||| |     |      |  |   | | |||| |   || ||  | || |  |          | | ||  |||||||| || || |||||  | |||||||||||||||||||  |||||||||||  ||||||| |||||||||||||| 
tttgcccttgcctgttt-ctat--taaacctctatgaacgtctcaatttaacacttatttt-tatgtcagttctaatatagtaaagaatatatatatca-tgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT

upper sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
ccttgcgtgttcattactgtaaagctcaacatgtgagaa-ggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgc-ctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
 |   |      ||    | |  |       |||   |    | | || ||| || | | |  |||| ||  | |||   |    |  || ||  | |||||||| || ||||||||  | |||||||||||||||||||  |||||||||||| ||||||| |||||||| ||||| 
-caaacaaaggaatcgaggcagtgggttttttgtattattaattagttccgttttctatgcc-ctgttattttgtttgttgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT

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|32948420|gb|BP184992.1|BP184992
EST:     GGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAG                         TGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
genomic: GGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAGgtgaggggaa ... ttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
EST: gi|29630401|gb|CB635410.1|CB635410
EST:     GGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAG                         TGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
genomic: GGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAGgtgaggggaa ... ttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
EST: gi|58667966|gb|CK056652.1|CK056652
EST:     GGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAG                         TGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
genomic: GGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAGgtgaggggaa ... ttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
EST: gi|58605307|gb|CK033340.1|CK033340
EST:     CCCCGAGGCCAAGCGCTGCGCGGCCTCCCGCACTGGCCAG                         TGTTATTTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCAT
genomic: CCCCGAGGCCAAGCGC-GCGCGGCCTCCCGCACTGGCCAGgtgaggggaa ... ttctctgcagTGTTA-TTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCAT
EST: gi|29622550|gb|CB627561.1|CB627561
EST:     GGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAG                         TGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
genomic: GGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAGgtgaggggaa ... ttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
EST: gi|29635958|gb|CB640967.1|CB640967
EST:     GGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAG                         TGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC
genomic: GGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAGgtgaggggaa ... ttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATC

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: 71 (upstream exon), 73 (downstream exon)
Score: 33

GGGGGCGCGCGATGAAGGAGAAGCGCGGGCTGGAAGCCGCGGCGGCCGGTGGCGACGGCCACCCCGAGGCCAAGCGCGCGCGGCCTCCCGCACTGGCCAGgtgaggggaa ... ttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
                          ttttttccgcttcgcc  CT-rich tract
                      atgatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- ttgcgtg
- - - - - - - - - - - - - - -catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatg