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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcctgctaaagtgcttctgttattgttactcctcctagtgcactccctaaatttgcttttgcagtgtcctaaccttctggcgttgatttgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC

Basic information

species Oryza sativa
transcript LOC_Os01g70960.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 5
-ttgcctgctaaagtgcttctgttattgttactcc-tcctagtgcactccctaaatttgcttttgcagtgtcctaaccttctggcgttgatttgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC
 ||   | |||  || | | | | ||| |  | |  | |   || |||       | | |||   |  | |  | |       |     | |   ||| |||||  | || ||  | ||||| ||||| ||||| |||||||| || || |||||||| || ||||||| |||||| || || || ||||||||||| ||||
atttagtacta--gttcatatatcattttgtccctataccgatgtactgatattgtgttcttaaacctttttttcatggctatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACTC

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
ttgcctgctaa-agtgcttctgttattgttactcctcctagtgcactccctaaatttgcttttgcagtgtcctaaccttctggcgtt--gatttgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC
 |   || ||  ||| | | | | ||| |   |||   ||  |   | |  | |||   || |  |   || |  | |      |||   | |   ||| |||||  | || ||  | ||||| ||||| ||||| |||||||| || || |||||||| || ||||||| |||||| || || || ||||||||||| || |
-tatatggtactagttcatatatcattttg--tccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
ttgcctgctaaagtgcttctgttattgttactcctcctagtgcactccctaaatttgcttttgcagtgtcctaaccttctggcgttgatttgaaatt-tagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC
  |      |   ||  |  | | |||| | || |   | ||| ||  ||  |||   ||    | ||| | | |||  || | ||||  |     | |||||||| || ||  |||| || ||||| || ||||||||||| || ||||| |||||||| ||||| || ||||| || || |||||||||||||| || |
ccgataatcatcttgacttgggttttgtca-tcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 5
ttgcctgctaaagtgcttctgttattgttactcctcctagtgcactccctaaatttgcttttgcagtgtcctaacc--ttctggcgttgatttgaaattt---agATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC
     |||| |  |  || | || ||  |  |  |     |   ||    |   |  | | | |     ||||| |  |   |  ||| |     | |||   |||| || ||||| ||||| |||||||| ||||||||||| ||||| || || ||||| || ||||| |||||||| ||| | |||||||||||||| || |
-----tgctgatttttttttattttttatgtttatggacatattctgttcatgatgacctattcctctacctaatcaatcaagttgttcacaaatatttttgtagATCCGAGAAGGGTTGCACTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGC

upper sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EDO96204 (Chlamydomonas reinhardtii), 3'ss of exon 7
ttgcctgctaaagtgcttctgttattgttactcctcctagtg---------cactccctaaatttgcttttgcagtg-tcctaaccttctggcgttgatttgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC
       || || |  |  ||  | ||| || || || |  |         ||||  |  || |     |    |    ||| ||| ||   ||       ||     |||| || || ||| || | ||||| ||||||||||| || || ||||| |||||||||||||||||  | || || |  || ||||| || || ||||| |
------tcttaattaatcatg--aatgtaaccccccccaaagagggtctaccactttcgtaactaatcatgaatgcaaccctcaccctcaaccgccacccggacgc--agATCCGCGAGGGCCTGTACTACAACCCCTACTTCCCGGGCGGCGCCATCGCCATGCCCAAGATGCTGGTGGACGGCGGTGTGGAGTACGAGGACGGCACGC

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|27920999|gb|CB096807.1|CB096807
EST:     GGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: GGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|86502387|gb|CI145020.1|CI145020
EST:     ACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCNTGGTGGTGCCATAGCC
genomic: ACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|218495259|gb|FG944818.1|FG944818
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|3766676|gb|AU030786.1|AU030786
EST:     ACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|29669775|gb|CB666050.1|CB666050
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|29669904|gb|CB666179.1|CB666179
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|87021720|gb|CI276119.1|CI276119
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|55432382|gb|CV729212.1|CV729212
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|29669776|gb|CB666051.1|CB666051
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|38481751|gb|CF965826.1|CF965826
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|313090494|gb|HO213490.1|HO213490
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCTTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|11564727|gb|AU165363.1|AU165363
EST:     TTTTTGCCCCTTCTCACTGGTTATCGTGATCCCACCTGCTGGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCCATAG
genomic: TTTTTG-CTCTTCTCACTGGTTATCGTGAT-CCACCTGCT-GGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTG-CCATAG
EST: gi|87029581|gb|CI257376.1|CI257376
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|117235872|gb|CT847828.1|CT847828
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|29669905|gb|CB666180.1|CB666180
EST:     ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCG                         ATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCC

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: 59 (upstream exon), 70 (downstream exon)
Score: 27

GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctct ... tgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctaaatttgcttttgcagtgtcctaaccttctggcgttgatttgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC
                                       ttgatttgaaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcctgctaaagtgcttctgttattgttactcctcctagtgcactccctaaatttgcttttgcagtgtcctaaccttctggcgttgatttgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-tgcctgc
- - - - - - -tgcttct
- - - - - - - - - - - - -tgttact
- - - - - - - - - - - - - - - - - - ctagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatt