Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT

Basic information

species Oryza sativa
transcript LOC_Os01g01710.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G036290_T02 (Zea mays), 3'ss of exon 10
aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatt-tgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
| || |   | | |    | ||||||    |      |  ||      |    | | ||     ||  ||      | |   || | |   | ||||||||| ||||||| ||||| |||||||||||||||||||| ||||||||||| ||||| || || || ||||||||  | ||||||||||||||||||||||||
agaaaacgaaaacgggttataaaattaaacaccgcacgatctcttaaatagtaagcattccatgtta-acagtttttgagcgttcactgacgttaatgcagGTTGGGTTCGCTGACGTTCAAAGCTCCTGACAATGTAAAATACCCGTCAATGGACCTAGCGTACGCAGCTGGGCGGGCTGGGGGCACCATGACAGGAGTT

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 10
------aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
       |||||  |  |  |  |  | | |  ||||    ||| | |||  | ||   ||  ||||| |     |    | |||| ||  | || | ||||||||| ||||||||||||||||||||||||| ||||| || |||||||| || ||||| || ||||||||||||||  | ||||||||||||||||||||||||
ctgcattaaagatgttaagacttcgcacagtc-ttaaacagtaggaatta--catggtaacagtttttgagcattca---gattaagttccagttggttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTT

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 10
aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataat--gcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
    |   | ||| ||   |||    |||| |    | | | | | |    ||   |     | |   || ||  |||  ||   | | ||    |  |||| || |||||| |||| |||||    || ||||||||||||||||| || |||||||| || ||||| |||||| ||||||| ||||| ||||| ||||||
ttttggtgtggat-cagttaaactgggttaggac-cactgccttatctatcagcattcagcacctaaaaccaaaagttgtttacaattgtggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 10
aaaagaactagatgcaacaaaaaattgttaagttatagtacttaa---ccgtgaagaccttttttcattgcacga-agggtt-aatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
       | ||||  ||||| ||||  |   || | | || | ||     |  |  |  || ||   ||||  || | | || || ||  |||   ||  |||||||| || ||||||||||| ||| ||||||||||||||||||| || || |||||||| |||||||| |||||| | ||||| ||||||||||||||||||
----tttccagattaaacaataaat-atggtgtgaaaataatgaaaacttgcaatcagtttattagtttgcttgacatgattgaaattggaatggaatggtgcagGCTTGGGTCACTGACATTTAAAACTCCTGACAATGTGAAATATCCATCCATGGATCTTGCCTATGCTGCTGGACGGGCTGGAGGCACCATGACAGGAGTT

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|86898927|gb|CI296156.1|CI296156
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|38478051|gb|CF962184.1|CF962184
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|88849804|gb|CI001510.1|CI001510
EST:     AGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAGATACCCGTCGAT
genomic: AGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|29613665|gb|CB618678.1|CB618678
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|29620640|gb|CB625651.1|CB625651
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|38478000|gb|CF962133.1|CF962133
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|58687978|gb|CK076665.1|CK076665
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|14982024|gb|BI306702.1|BI306702
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|86258828|gb|CI000057.1|CI000057
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|29688465|gb|CB684740.1|CB684740
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|58674748|gb|CK063435.1|CK063435
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|218502386|gb|FG960211.1|FG960211
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|89184692|gb|CI007117.1|CI007117
EST:     AGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTG-AATACCCGTCGAT
genomic: AGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|10423679|gb|AU108198.1|AU108198
EST:     ATCTANTTGCTCAGAGGTCTACCTGGCCCCGACTAGATCTTTGC-A                         GCTGGGTTCACTGACATTCAAAAGCTCCTGACAATGTGAAATACCCGTCGA
genomic: ATCTA-TTGCTCAGAGGTC-ACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTC-AAAGCTCCTGACAATGTGAAATACCCGTCGA
EST: gi|29620627|gb|CB625638.1|CB625638
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|58677119|gb|CK065806.1|CK065806
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|29620628|gb|CB625639.1|CB625639
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|88963579|gb|CI029373.1|CI029373
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|86502359|gb|CI144992.1|CI144992
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|89187005|gb|CI053408.1|CI053408
EST:     CAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: CAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|38475522|gb|CF959655.1|CF959655
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGA
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGA
EST: gi|29620642|gb|CB625653.1|CB625653
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|29617050|gb|CB622062.1|CB622062
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|58594821|gb|CF993129.1|CF993129
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|58595068|gb|CF993376.1|CF993376
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT

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), 71 (downstream exon)
Score: 57

TGGGATGGCCAGATATGCGGATACCAATCTTATACACCATGTCTTGGCCAGACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
                               ttaatttttaatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
aaaagaa
- - - - - - - caacaaa
- - - - - - - - - - - - - - - - - - - - - - -ccgtgaa