Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgcatgatcttaattttactcctatgttaagtgttgtcctatagatctgtacctgtttgaagagagaacttataatttgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA

Basic information

species Oryza sativa
transcript LOC_Os12g30020.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 2
gattgcatgatcttaattttactcc--tatgttaagtgttgtcctatagatctgt---acctgttt-----gaagagagaacttataatt-tgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
             || ||| |||||   |   ||||| ||||| ||||    |||   |  |||||       |    |  |  ||| || || |   |  || | |||||| ||||||||||||||| |||||||||||||| ||||||||||| || ||||| |||||||| |||||||| ||||| ||||| ||| |||||||||| |
-----------tatagtttaactccatcaaactaagtattgtcttatactgttgtgttatttgttttttatagaatatgtgccaatacttctgaatctaatgtccatacagATAATTGCCACAGTTTGTATGTTCTTGGCTGGGAAAGTTGAAGAAACACCTAGACCTTTGAAGGATGTTATCCTGGTATCTTACGAGCTTATTCATAAGA

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 3
gattgcatgatcttaattttactcct--atgttaagtgttgtcctatagatctgtacctgtttgaagagagaacttataat----ttgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
       |     ||  |||||||||  | | || || |   | | | ||        |||||  | ||| |  |   |||    ||| |   |   | |  ||||| ||| || || ||||| || ||||||||||||||||||||||| || ||||  |||||||| ||||| ||  |||||||||| | ||||||| |||| |
------ttagatatagatttactccttcaagctaggtatcaccatgtggaatgtattttgtttctaaagaaaggtaccaatacttttgaatctaatatccacacagATAATCGCTACTGTTTGTATATTCTTGGCTGGAAAAGTTGAAGAAACACCTAAACCTTTGAAGGATGTCATCGTGGTTTCTTACGGGATTATTAATAAGA

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 2
gattgcatgatcttaattttactcctatgttaagtgttgtcctatagatctgtacctgtttgaagagagaacttataatttgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
   | | | || |  |||       | |      |   |   ||||| | |  |  |   | ||   | |||| ||||||            | || ||||| ||||| || || || |||||| | ||||| || ||||||||||| ||| | ||  | || ||||||||||| |||||||||||||| ||||| || |
aggttcctaatttatattaagagaatgtagatgttaaagctgtatagttttaaagattacttaatcaaaaactcataattcacttgatgaacttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 2
gattgcatgatcttaattttactcctatgttaagtgtt---gtcctatagatctgtacctgtttgaagagagaacttataatttg--tactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
   | | | || |  || |||     ||| ||  ||||   |   ||||  | |  |  |   | ||   | | || ||||||    |  ||| | || || ||||| ||||| || || || |||||| | ||||| || ||||||||||| ||| | ||  | || ||||||||||| |||||||||||||| ||||| || |
---ttcctaattt--atattaagagaatggtagatgttaaagcattataattttaaagattacttaatcaaaatctcataattcacttgatgaacttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 3
-gattgcatgatc--ttaattttactcctatgttaagtgttgtcctatagatctg--tacctgtttgaagagagaacttataatttgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
    ||||  ||   | |||| |  |  | |||||  | || |      ||      |||  |  |    |  || ||     ||  |  ||    ||  | ||||| ||||| || || ||||||||| | |||||||| ||||| || || ||  |||| ||||||||||||||| | || || |||||||||||  | || |
tctatgcagaattagtgaattgtgattgt-tgttatttcttctagagcggaaaaaaatactcggatctttactgagctctctcttcatgttg----tttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 4
--gattgcatgatcttaattttactcctatgttaagtgttgtcctatagatctgtacctgtttgaagagagaacttataatttgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
    ||   ||  | ||  ||||  | | |   || |   |    | ||   |     | ||            ||  |  |||| ||  |   ||   ||||| ||||| ||||| ||||||||| | || |||||||| ||||| || |||||||| || |||||||||||| | || || |||||||| || || || |
ctagttctttgtccata--tttatccttctagaaactagcgcagaacagtattaagattattactgagtcctttttccatgttgtcctccctcctcacccagACGATTGCTACAGTCTGCATGTTCCTTGCGGGAAAAGTGGAAGAAACTCCTAGGCCGTTAAAAGATGTTATTGTTGTCTCCTATGAGATAATACACAAGA

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 2
gattgcatgatcttaattttactcctatgttaagtgttgtcctatagatctgtacctgtttgaagagagaacttataatttgtactgaccgtt------cttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
   ||||||     ||   ||     |  | || |      | | ||||  ||   | ||  |   ||    || | ||   |||   |  |        |||||||| || |||||||| ||||||||| | || || || ||||||||||| ||  | ||  |||| |||||||| || ||||| ||||| || ||||||||||
---tgcatgggaagaaaagtagataaaaatgaaatac---gcaagagattagttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAA

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|86904853|gb|CI310646.1|CI310646
EST:     TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA                         ACAATTGCCACAGTTAGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
genomic: TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGAgtaagtactt ... gttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
EST: gi|33674887|gb|CF303126.1|CF303126
EST:     TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA                         ACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
genomic: TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGAgtaagtactt ... gttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
EST: gi|33675720|gb|CF303959.1|CF303959
EST:     TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA                         ACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
genomic: TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGAgtaagtactt ... gttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
EST: gi|58656723|gb|CK045403.1|CK045403
EST:     GTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA                         ACAATTGCCACAGTGTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
genomic: GTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGAgtaagtactt ... gttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
EST: gi|29677818|gb|CB674093.1|CB674093
EST:     TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA                         ACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
genomic: TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGAgtaagtactt ... gttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
EST: gi|58668632|gb|CK057318.1|CK057318
EST:     TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA                         ACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT
genomic: TCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGAgtaagtactt ... gttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCT

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: 75 (upstream exon), 74 (downstream exon)
Score: 26

GCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGAgtaagtactt ... gttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatctgtacctgtttgaagagagaacttataatttgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
                                     tactgac  putative branch site (score: 26)
                                           ccgttctt  CT-rich tract
                        aacttataatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgcatgatcttaattttactcctatgttaagtgttgtcctatagatctgtacctgtttgaagagagaacttataatttgtactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- -tgcatga
- - - - - - - - - - - - ctatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtactg