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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcaaacaaaacaccctggtttatcctgcaaggcttggtttttccagttcgtcgcctgaaactttatctgccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGCCTATTGGCTGGTGATTTCACTTCCAATCTCAAGCTCCTGCAGAACTACC

Basic information

species Oryza sativa
transcript LOC_Os01g68010.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 8
----gtagcaaacaaa-acaccctggtttatcctgcaaggcttggttt--ttccagttcgtcgcctgaaactttatctgccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGCCTATTGGCTGGTGATTTCACTTCCAATCTCAAGCTCCTGCAGAACTACC
    |  || | |    ||||  |   || | ||       |   |||   ||   ||| | |||| ||||||| ||||| ||   ||||| |||||||||||||| ||||| || |||||||| |||||||| || |||||  |||| || || ||||| ||||| ||||||||||||||||| ||||
gtgagccgcgagcgcgcacactgtttcttctgctctggaattatctttggctctgtttctttgcct-aaactttgtctgctgaacacagGAAACCTTGCTCAGAATATGCTGCGCGATGCTGATCCTTGTCCGGAAGCGCCTCCTGGCCGGCGACTTCACCTCCAACCTCAAGCTCCTGCAGAATTACC

upper sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G00430.1 (Glycine max), 3'ss of exon 8
----------------gtagcaaacaaaacaccctggtttatcctgcaaggcttggtttttccagttcgtcgcctgaaactttatctgccga------gtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGCCTATTGGCTGGTGATTTCACTTCCAATCTCAAGCTCCTGCAGAACTACC
                 |      ||||| | |  |  | || || | |  ||  ||      |         | | ||  ||| |||  |       ||| |||||||  | |||||||| |||||||||||||| ||||| || || | ||||||  | || |||||||||||||| || |||||| | ||||| |  || |
ttatgtgttgattttctttttcctcaaaatatctag--taattcttcca--ctcagtgaaaaaatagaaaaagcaggaaaattaactgatgcaatactgtgtagGAGACACTTCTCAGAATATGCTGTGCAATGCTAATTCTCGTTCGTAGACGCCTTCTAGCGGGTGATTTCACTTCTAACCTCAAGATGCTGCAAAGTTATC

upper sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 8
----------gtagcaaacaaaacaccctg------gtttatcctgcaa--ggcttggtttttccagttcgtcgcctgaaactttatctgccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGCCTATTGGCTGGTGATTTCACTTCCAATCTCAAGCTCCTGCAGAACTACC
              ||||   ||     |       || |||  ||| |   |  || |||| | ||||  |    | | | |     | |    ||||||||||  | ||  |  | ||||||||||||||| |||| || || || |||||  | || |||||||||||||| ||||||||| | ||||| || || |
ctagaagatgaagacaaatttaagtttttatcaactgtatattttgctattagactgcttttacaagttgtttttttcataatggtgatccactctgcagGAGACTCTTCTTCGGGTATGCTGTGCAATGCTGGTTCTCGTTCGTAAGCGCCTCCTTGCGGGTGATTTCACTTCTAATCTCAAGTTGCTGCAAAATTATC

upper sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 8
-------gtagcaaacaaaacaccctggtttatcctgcaaggct-tggtttttccagttcgtcgcc----------tgaaactttatctgccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGCCTATTGGCTGGTGATTTCACTTCCAATCTCAAGCTCCTGCAGAACTACC
        || ||  | |  | | |    ||||  |    | |  |  | | || ||  |    |           | ||| ||| | |  | | | ||||||||  ||||  | || || ||||||||||||||||||||||| |  || || ||||| |||||||||||||| ||||||||||| || || |||||||
tccctaactaccaggcgatgccctccatattataatcattgacaatcatctgtctagaaccaaacgaatgtataaataaaagtttttattgcaatttcagGAGACACTGCTTCGGATATGTTGTGCAATGCTGATTCTTGTCCGGAGGCGACTGTTGGCAGGTGATTTCACTTCGAATCTCAAGCTGCTCCAAAACTACC

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|88510088|gb|CI437594.1|CI437594
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88514084|gb|CI441590.1|CI441590
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88282474|gb|CI403870.1|CI403870
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88474029|gb|CI411300.1|CI411300
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|86422689|gb|CI060262.1|CI060262
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88376725|gb|CI538029.1|CI538029
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88383076|gb|CI538104.1|CI538104
EST:     ACACTATTCACATATGGGACACACTATTAANTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88480849|gb|CI418120.1|CI418120
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88504579|gb|CI432085.1|CI432085
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|9866163|gb|AU101913.1|AU101913
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88479607|gb|CI416878.1|CI416878
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88981591|gb|CI027202.1|CI027202
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88903574|gb|CI089112.1|CI089112
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|44674637|gb|CR288071.1|CR288071
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGC
EST: gi|88282586|gb|CI403982.1|CI403982
EST:     ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAG                         GAGACCTTGCTCAGAATCTGCTGGTGCNAATGCTGATTTCTTGTCCGAAAA
genomic: ACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCT-GTGC-AATGCTGA-TTCTTGTCCGAAAA

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: 46 (upstream exon), 40 (downstream exon)
Score: 2

CGCATTCCGGTGGATTACGCTACTGTTAACCCAGGAGTTCAACTTTGCTGACACTATTCACATATGGGACACACTATTAAGTGATCCTGATGGTCCTCAGgtagcaaaca ... ccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGCCTATTGGCTGGTGATTTCACTTCCAATCTCAAGCTCCTGCAGAACTACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcaaggcttggtttttccagttcgtcgcctgaaactttatctgccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGCCTATTGGCTGGTGATTTCACTTCCAATCTCAAGCTCCTGCAGAACTACC
                                 aaactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcaaacaaaacaccctggtttatcctgcaaggcttggtttttccagttcgtcgcctgaaactttatctgccgagtgcagGAGACCTTGCTCAGAATCTGCTGTGCAATGCTGATTCTTGTCCGAAAACGCCTATTGGCTGGTGATTTCACTTCCAATCTCAAGCTCCTGCAGAACTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG