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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccccggaaaagttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC

Basic information

species Oryza sativa
transcript LOC_Os01g62650.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G04060.2 (Glycine max), 3'ss of exon 9
ccccccggaaaagttgcattcaacattctg-atctctctgtttttttgtttttg----tttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
      |    ||||  |   |||  || | |  |||        ||| |  |     |  ||  ||  || || || | | | | |      |   |  ||||||| |||||||| ||||| || |  |||||||||||||| || || ||||||||||||||||| || ||||| ||| | || || |||||| | || ||||
-----tgctctagttataccaaactctcagcacatcttgacaaaattgatagtaggactcattcattccttcttatgatatatatcttgttcctcttatatgcagGCAATGATGAAAGATCAATTCGCCAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAACAGCGAGAGCTAATTCTTTCACGAATTAAAGTTC

upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G14500.1 (Glycine max), 3'ss of exon 9
--ccccccggaaaa-gttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
  |     ||  || | |  | | |||   | || |          | |    | | | ||| |||||       |  |   |  ||    |   |  ||||||| |||||||| ||||| ||||  || || |||||||| || || ||||| |||||||||||||| || |||||| |||| || || ||| | |||||||
gtcagtgtggcgaatgctttagttaactcccagaaccaca---acctgtaaaatagatcttggtttgtcacaaaatgataaatcagattccttttatatgcagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G14550.1 (Glycine max), 3'ss of exon 10
--ccccccggaaaa-gttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
  |     ||  || | |  | | |||   | || |          | |    | | | |||  ||||       |  |   |  ||    |   |  ||||||| |||||||| ||||| ||||  || || |||||||| || || ||||| |||||||||||||| || |||||| |||| || || ||| | |||||||
gtcagtgtggcgaatgctttagttaactcccagaaccaca---acctgtaaaatagatcttggcttgtcacaaaatgataaatcagattccttttatatgcagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA12G06450.1 (Glycine max), 3'ss of exon 8
-ccccccggaaaagttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
 |  || | ||||  |  ||      ||   |  | | |         ||||   |  |     |||| |     |  |   | | |      |  | ||||| |||||||| ||||| ||||  || || |||||||| || || ||||| |||||||||||||| ||||| ||| |||| || || ||| | |||||||
acaacctgtaaaaaatagatcttggtttgccacttgtttaaagaggc-ttttccctcctccccagtttctcgaaatgataaatcagattccttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G14530.1 (Glycine max), 3'ss of exon 8
ccccccggaaaagttgcattcaacattctgatctctctgttttttt-----gtttttgtttttgttttgtttttgtgttttttt---tttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
        | ||  || |    | ||  || | | ||  || ||       |   ||  || |       |||||     |  |   |  ||    |   |  | ||||| |||||||| ||||| ||||  || ||||||||||| || || ||||| |||||||||||||| || |||||| |||| ||||   || | |||||||
--------acaacctgtaaaatagatcttggtttgtcacttgttcaaagaggcacttccttcttccccagttttgcaaaatgatgaatcagatttttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC

upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
ccccccggaaaagttgcattcaacattctgatctct--ctgtttttttgtttttgtttttgttttgttttt----gtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
      |     | |||  | || ||| || |   |   || |||  || ||  ||     | | ||| ||       || || || |      |    | |  |||| |||||||| ||||||||||  |||||||||||||| || || ||||||||||||||||| |||||||||||| ||||| |||| ||| | |||||||
------gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgttcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC

upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
--------------ccccccggaaaagttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
              ||  ||        ||||     || |  |    | |||    |     |        | |  |  |  |  |  |  |     | |  | |   ||||||||||||||||||| |||||||| ||||| || || ||||| || ||||||   ||    ||  ||||||| ||| |||| ||| | |            
cgcccaccattctgccttccccgccttctgcaccgcgcactgcg-cggcactggccctgcaactcc-cccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------

upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ32290 (Selaginella moellendorffii), 3'ss of exon 5
ccccccggaaaagttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
                                                    ||            ||||||  |   ||   | | ||     || ||||| ||||||||||| || ||||  ||||| || || |||||||||||||||| |||||| || |  ||| | ||  |  |  || | ||  | || ||||
----------------------------------------------------gtaggaaagaaagatttgtgactccattcatatacatccttttttcagGCTATGATGAAGGACCAATTTGCCAACTACGTGGTGCAGAAAGTACTGGAGATTTGTGACGACCGCCAGAGGGAAATTCTTTTGACTCGTATCAAAGTTC

upper sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ20967 (Selaginella moellendorffii), 3'ss of exon 5
ccccccggaaaagttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
                                              ||          | |||||       |   ||  |  | | ||     || ||||| ||||||||||| || ||||  ||||| || || |||||||||||||||| |||||| || |  ||| | ||  |  |  || | ||  | || ||||
----------------------------------------------gtaggaaagaaagatttgtgaccccctccattcat--atacatccttttttcagGCTATGATGAAGGACCAATTTGCCAACTACGTGGTGCAGAAAGTACTGGAGATTTGTGACGACCGCCAGAGGGAAATTCTTTTGACTCGTATCAAAGTTC

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|87040335|gb|CI194957.1|CI194957
EST:     TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
genomic: TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
EST: gi|87016447|gb|CI273657.1|CI273657
EST:     TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
genomic: TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
EST: gi|58656359|gb|CK045039.1|CK045039
EST:     TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
genomic: TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
EST: gi|29633935|gb|CB638944.1|CB638944
EST:     TGACGAGAATGAGCTTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGAACAGAAAGTACTGGAG
genomic: TGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
EST: gi|29627677|gb|CB632688.1|CB632688
EST:     TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
genomic: TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
EST: gi|29633937|gb|CB638946.1|CB638946
EST:     TGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
genomic: TGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
EST: gi|29622762|gb|CB627773.1|CB627773
EST:     TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
genomic: TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
EST: gi|29645189|gb|CB650196.1|CB650196
EST:     TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
genomic: TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
EST: gi|29622960|gb|CB627971.1|CB627971
EST:     TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAG                         GCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG
genomic: TTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAG

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: 73 (upstream exon), 73 (downstream exon)
Score: 31

AAATGTTGTTGAGAAGTGTTTAACATTTGGCGGACCTGCAGAGCGGGAAGTTCTTATAAATGAAATGCTCGGAACTACTGACGAGAATGAGCCTCTTCAGgttttcatta ... acacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC
                                        aaataac  putative branch site (score: 31)
        tttttgttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccccccggaaaagttgcattcaacattctgatctctctgtttttttgtttttgtttttgttttgtttttgtgttttttttttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC

- - - - - - - tgcattc
- - - - - - - - - - - -cattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata