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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcgacgacatctatgattttagatgatattccttggtttttatactgaacatgtctacaatttggttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g34860.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 9
CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcgacgacatctatga------ttttagatgatattccttggtttttatactgaacatgtctacaatttggttgcag
 |||||||||||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||||||| || || || |||||||| ||| |  | ||||| |||| | || |     |||       | ||  ||||||| |||   || |||  |||| ||| | | |||||   ||||||
TAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGATTAACAATCTTCAGgt-acatgcaacaattctcatggagaaattgtttaatgatat-cctgatttcttaatctgatcatctgtgcaattaaattgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G10060.1 (Glycine max), 5'ss of exon 9
CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgt------tacattcgacgacatctatg-----------attttagatgatattccttggt-ttttatactgaacatgtctacaatttggttgcag--------------
||| ||||||||||||||||||||||| ||||| ||||| ||||| || |||||||| ||||||||||| || || |||||||| || |||||  |||||||      || | |     | |    ||           | | ||| |  |||    |  | |||| |  ||||  |  | |  | ||| ||                  
CAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAATAAACGATCTGCAGgtattaaatataattagaaatactagtgcaatcataactagtctaggtcctatgttgtcatattttgttttgaaagttaccaacacttgtttttccccttgtcaatgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA18G52890.1 (Glycine max), 5'ss of exon 11
CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgt--tacattcgacgacatctatgattttagatgatattcct-tggtttttatactgaacatgtctacaatttggttgcag-------------------------------
||||||||||||||||||||||||||| ||||| ||||| ||||| || |||||||| |||||||||||||| || |||||||| || |||||  |||||||  || ||   |  | |  ||    |  |     || |  | | | | ||||  ||  ||| | |    ||||   |                                  
CAATTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCACTCACTGATGAGGAAATAAACGATCTGCAGgtattaaatattattagaattactggtgcaatcattactagtctaggtcttatgttgt-catattt-tgttttgaaagttaccaacacttgttttaccccttgtcaatgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 5'ss of exon 9
CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgt----tacattcgacgacatctatgattttagatgatattc---cttggttttta-tactgaacat--gtctacaatttggttgcag------------
||||||||||||||||||||||||||| || || || ||  ||||||| ||  |||| ||||| ||||||||||| ||||||||||| || ||  |||||||     |  ||  | |   | | |     ||  |  ||||    |||| ||  |  || | |        ||  ||||||| |                
CAATTTCACCAACAAGAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGATAAATGAGTTGCAGgtatgtcatgtttaagggattttgtacaagtaattagtattttgtcttgattgctggtaataactgataacctggaatttggctatgattctgggtgtag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv19s0027g01480.t01 (Vitis vinifera), 5'ss of exon 4
CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgt--tacat-tcgacgacatctatgattttagatgatattccttggttttta----tactgaacat--gtctacaatttggttgcag------------
||||||||||||||||||||||||||| || || || ||  ||||||| ||  |||| ||||| ||||||||||| ||||||||||| |||||  |||||||  | ||| |  | |  || | |     |   |  |||| | |  |  |||    || |||  |     ||  ||||||| |                
CAATTTCACCAACAAGAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGATAAACGAGTTGCAGgtatttcatgtttaggggatttgtacaagtgattagtatttcgtcttgattacgggtaatgactaataacctgaaatttggctttgattctgggtgcag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 5'ss of exon 9
CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgt----tacattcgacgacatctatgattttagatgatattccttggttttta----tactgaacat--gtctacaatttggttgcag-------------
||||||||||||||| ||||||||||| || || || ||  ||||||| ||  |||| ||||| ||||||||||| ||||||||||| || ||  |||||||     |  ||    |   | | |     |   | ||||| | |  |  |||    || |||  |     ||  ||||||| |                 
CAATTTCACCAACAACAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGATAAATGAGTTGCAGgtatttcatgtttaggggattttgtacaagtgattaatatttcgtcttgattacaggtaatgactaataacctggaatttggctatgattctggggtgcag

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|29629252|gb|CB634263.1|CB634263
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88470031|gb|CI407302.1|CI407302
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAN                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|58695333|gb|CK084020.1|CK084020
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86494911|gb|CI137544.1|CI137544
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88221899|gb|CI221855.1|CI221855
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86493496|gb|CI136129.1|CI136129
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|24468878|gb|CA305827.1|CA305827
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|29661307|gb|CB657582.1|CB657582
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88202077|gb|CI202432.1|CI202432
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86493622|gb|CI136255.1|CI136255
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|29662501|gb|CB658776.1|CB658776
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88491765|gb|CI429037.1|CI429037
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88223742|gb|CI223591.1|CI223591
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88832351|gb|CI019292.1|CI019292
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGCTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|29632929|gb|CB637938.1|CB637938
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|89189364|gb|CI048903.1|CI048903
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86501835|gb|CI144468.1|CI144468
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88466031|gb|CI519904.1|CI519904
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86541540|gb|CI181746.1|CI181746
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88991649|gb|CI019827.1|CI019827
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86499426|gb|CI142059.1|CI142059
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAAATGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88961812|gb|CI096965.1|CI096965
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86434161|gb|CI094504.1|CI094504
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86502413|gb|CI145046.1|CI145046
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|86423293|gb|CI060866.1|CI060866
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
EST: gi|88248226|gb|CI248075.1|CI248075
EST:     ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAG                         TGGAATGCCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA
genomic: ATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGA

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: 69 (upstream exon), 74 (downstream exon)
Score: 28

CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcg ... ttggttgcagTGGAATGTCAGAGAAGAGGTGCAAAATAAACTGAAAGTTGAGTTGAGATGAAATAGAGCTAGTTCACGTGTTCGACCAGACATTGATTGTTTGACCATTT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGATCAACGACATGCAGgttacattcgacgacatctatgattttagatgatattccttggtttttatactgaacatgtctacaatttggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA