Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaataacattttatgttgaatgccattcacgtttacgttttagattttattgtgctggatattgttggcacatttagttacatttatttctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA

Basic information

species Oryza sativa
transcript LOC_Os07g19190.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g19190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
-taaataacattttatgttgaatgccattcacgtttacgttttagattttattgtgctggatattgttggcacatttagttacatttatttctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA
 | | |  || ||  | |  | |    ||  |   |       |  ||||||    |    | | || | |||   |   || ||    |||  || |||||| ||||| || ||  | || ||||| || || || |||||||||||||||||||||||||| || ||||||||||| || |||||| | |||||||| |
ttgattggcacttcttatatattattgtttgctcatcaaaaaaatgttttatacccccaactgtagt-gccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA

upper sequence: LOC_Os07g19190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S343_39V6.1 (Physcomitrella patens), 3'ss of exon 1
taaataacattttatgttgaatgccattcacgtttacgttttagattttattgtgctggatattgttggcacatttagttacatttatttctg------ttcg--cagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA
         ||||  |||  ||   |    | |||   |  | |  ||   | || |||| | || ||   | |||  || | | | |  |||      || |  ||||| ||| | ||||||||||| |||||||| || ||||| ||||||||  | |||||||||||||| || |||||||||||||| ||     | ||||| |
------tgcttttgcgtttgat-ttaagggcttttgtttcgtggtattggctttg-tggacactgatgaagcttttgattgcgtgtctgcctgacttgttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGAAATCCTCGTAAGGTGAAGTGGACAAAAGCGTATAGAAAGCTTCATGGAA

upper sequence: LOC_Os07g19190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S43_13V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------taaata-acattttatgttgaatgccattcacgtttacgt---tttagattttattgtgctggatattgttg-gcacatttagttacatttattt--ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA
                        |   ||  |   | | ||    ||   |||| |||  |||   | ||| |||| |       |||| ||    |  | |     |   | | |||     | || |||| ||| | ||||||||||| ||||| || || ||||| ||||||||  |||||||||||||||| || ||||| |||||||| |||    | || || |
gtctgtttgctctcccaatgtggattcctatgctgctgacgtgatttggagttcatgttggcgtggctgtaggttttgtgactgacgatactgaaatgttcgtacgcctctgtctgtttggtcatgcgaagATATTTAGGTTTTGCCGGTCGAAATGCCACAAGAATTTTAAGATGAAACGGAATCCTCGTAAGGTGAAGTGGACCAAAGCGTATAGGAAGCTTCACGGCA

upper sequence: LOC_Os07g19190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ21089 (Selaginella moellendorffii), 3'ss of exon 1
taaataacattttatgttgaatgccattcacgtttacgttttagattttattgtgctggatattgttggcacatttagt-tacatttatttctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA
                                             | | |  |    |   |  | |  | |    | | || | |   |   | ||  |||||||||| || ||||| || || || || || ||||||||||||||||| |||||||| ||||| || ||||| ||    ||  |     | || || |
--------------------------------------------gtatgagcgcttcgatcacagatttctcgcgaaatataaaatcgctg--gctcttagATCTTTCGATTCTGCCGCTCCAAGTGCCACAAGAATTTCAAGATGAAGAGAAATCCTCGCAAGGTGAAGTGGACGAAGATCTATCGCAAGCTCCACGGCA

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|29628204|gb|CB633215.1|CB633215
EST:     GTCCGCAACGACGCCCAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: GTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|88372508|gb|CI610831.1|CI610831
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|86904503|gb|CI308713.1|CI308713
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCGAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|58688852|gb|CK077539.1|CK077539
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|88350896|gb|CI619154.1|CI619154
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|58675839|gb|CK064526.1|CK064526
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|55412205|gb|CV724581.1|CV724581
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|218479728|gb|FG953387.1|FG953387
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|163917855|gb|EG714749.1|EG714749
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|9865927|gb|AU101677.1|AU101677
EST:     GTCTACCCCCGGCCCACGGCATCCAGTTCGTCCCGGAACGACCGCCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAAATGTCTTANAAATTTTCAAGATGAAG
genomic: GTCTA-CCCCGG-CCACGGCATCCAGTTCGT-CCGGAACGA-CG-CCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTC-AAAATGTCATA-AAAATTTCAAGATGAAG
EST: gi|58030381|gb|CX727924.1|CX727924
EST:     TCCGCAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: TCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|58591169|gb|CF989477.1|CF989477
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|58589775|gb|CF988083.1|CF988083
EST:     CCACCGTCTACCCCGGCAACGGCATCCAGTTCGTCCGCAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
EST: gi|4881050|gb|AU065349.1|AU065349
EST:     CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAG                         ATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG
genomic: CCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGG

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), 71 (downstream exon)
Score: 29

GTAGTTCGGAGGCGGCGCGATGAGGTTGGAGAAGTGCTGGTTCTGCTCGTCCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctg ... ctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattgtgctggatattgttggcacatttagttacatttatttctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA
                                      tttatttct  CT-rich tract
                           atttagttacatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaataacattttatgttgaatgccattcacgtttacgttttagattttattgtgctggatattgttggcacatttagttacatttatttctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA

- aataaca
- - - - - - - - -tgaatgc
- - - - - - - - - - - - cattcac
- - - - - - - - - - - - - - - - - - - - - - - - - - gtgctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggc