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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatatttttttaatcttcaatgtattctccaaaatatgttgcataatgcttatttcagaataaaaaatacaactgtactgatatggttaattatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCGGCCATCGTTGGTGGATCCAAGGTCTCAACTAAGATTGGGGTGATTGAGT

Basic information

species Oryza sativa
transcript LOC_Os02g07260.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G382914_T03 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------taatatttttttaatcttcaatgtattctccaaaatatgttgcataatgc--ttatttca-gaataaaaaatacaactgtactgatatgg-ttaattatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCGGCCATCGTTGGTGGATCCAAGGTCTCAACTAAGATTGGGGTGATTGAGT
                                                                  |||   |||| ||   |||||   |  |    |||| | ||  | | | |  || |||||  |||||||||   ||   |    | |||  || ||||| ||||||||||||||| ||||||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| || |||||||
gtaataaaatgtcacccatgctcatgatcttttaagtatatttaggtactgttcagtaggatggggtaaatattttctacctttcaaaagagaccaataaatctttttaacatttcagttttttcataaataaaaaaggaaagatttgacaaatgactttattatctcagGAACTTGACTACCTTGTTGGAGCTGTTGCCAACCCAAAGAAGCCATTTGCCGCCATTGTTGGTGGATCCAAGGTCTCAACTAAGATTGGTGTCATTGAGT

upper sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G17600.1 (Glycine max), 3'ss of exon 4
--taatatttttttaatcttcaatgtattctccaaaatatgt-tgcataatgcttatttcagaataaaaaatacaactgtac-tgatatggttaattatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCGGCCATCGTTGGTGGATCCAAGGTCTCAACTAAGATTGGGGTGATTGAGT
  |  ||     |      | | |||   || ||  |||||  ||     |  ||  |  |   ||   | |  |    |   | || || |||||| |||||||||||||||||||| |||||||||||  ||||||| ||||  |||||||| || ||||||||||| || ||||| ||  | |||||||| || |||||||
gtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATCGTTGGTGGGTCAAAGGTGTCTTCCAAGATTGGAGTTATTGAGT

upper sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 3
taatatttttttaatcttcaatgtattctccaaaatatgttgcataatgcttatttcagaataaaaaatacaactgtactgatatggttaattatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCGGCCATCGTTGGTGGATCCAAGGTCTCAACTAAGATTGGGGTGATTGAGT
     | |||  ||| | ||   ||      | | ||| ||     |||  | | |     | |   ||   ||| |    |  || || ||| | |||||||||||| || ||||| |||||||| |||||||| |||||||| ||||| ||||| ||||| || || ||||| ||||| |||||||| || |||||||
----gtatttaaaatttgcagcataa-----agagtatcttcttagatgagtctctttattttactgatcagactatt---acttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT

upper sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 3
taatatttttttaatcttcaatgtattctccaaaatatgttgcataatgcttatttcagaataaaaaatacaactgtactgatat--ggttaattatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCGGCCATCGTTGGTGGATCCAAGGTCTCAACTAAGATTGGGGTGATTGAGT
   || | | | ||     |||     || ||   || |||   |  || |||    |        | |  |  ||   | | ||  | ||  |  ||| ||||||||||||| ||||||||||||||  ||||||| |||| ||||||||| || || |||||||| || ||||| ||| | || ||||| |||||||| |
-cttaatgtatgaagtccaaatagtggctacacc-taggttttcttttgtttagaatacttctttgagtttacttgacataacatttgttttctggttttagGAACTTGACTACCTTGTTGGAGCTGTGTCAAACCCCAAGAGGCCATTTGCTGCAATTGTTGGTGGCTCGAAGGTGTCATCGAAAATTGGAGTGATTGAAT

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|14191674|gb|AU183885.1|AU183885
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|33678660|gb|CF306899.1|CF306899
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|58605824|gb|CK033857.1|CK033857
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|13806339|gb|AU181481.1|AU181481
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAA                         GAACTTGACTATCTTGTTGGAGCTGTTGCAA-CCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|33794797|gb|CF323278.1|CF323278
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|29676664|gb|CB672939.1|CB672939
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|300216018|gb|HO088644.1|HO088644
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|29671336|gb|CB667611.1|CB667611
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|163918048|gb|EG713148.1|EG713148
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|29614437|gb|CB619450.1|CB619450
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|33793275|gb|CF322518.1|CF322518
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGGAGCTGTTGCAAACCCAAAGAAGCCATTTGC
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGG-AGCTGTTGCAAACCCAAAGAAGCCATTTGC
EST: gi|33690622|gb|CF318861.1|CF318861
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|33795493|gb|CF323616.1|CF323616
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|58667980|gb|CK056666.1|CK056666
EST:     TAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAA
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAA
EST: gi|33805002|gb|CF328378.1|CF328378
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|29656155|gb|CB652430.1|CB652430
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|86904967|gb|CI289114.1|CI289114
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|29656603|gb|CB652878.1|CB652878
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|14574908|gb|AU197198.1|AU197198
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCNTCCTGATGCAGAAG                         GAACTTTGACTATCTTTGTTGGGANCTGTTGCAAANCCAAAGAAGCCATTT
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTT-GACTATCTT-GTTGG-AGCTGTTGCAAACCCAAAGAAGCCATTT
EST: gi|33692729|gb|CF320968.1|CF320968
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|13904803|gb|BF889441.1|BF889441
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAA                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|427571|gb|D23639.1|D23639
EST:     GGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|38478259|gb|CF962392.1|CF962392
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|32947941|gb|BP184513.1|BP184513
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGA
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGA
EST: gi|33679224|gb|CF307463.1|CF307463
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCT
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCT
EST: gi|4878615|gb|AU062914.1|AU062914
EST:     GAGTTACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAGGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|117247218|gb|CT848558.1|CT848558
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|87020408|gb|CI263271.1|CI263271
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|14574727|gb|AU197242.1|AU197242
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
EST: gi|27554292|gb|CA998192.1|CA998192
EST:     GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG
genomic: GAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaa ... attatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcttatttcagaataaaaaatacaactgtactgatatggttaattatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCGGCCATCGTTGGTGGATCCAAGGTCTCAACTAAGATTGGGGTGATTGAGT
                                              ttatttc  CT-rich tract
     ttatttcagaataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatatttttttaatcttcaatgtattctccaaaatatgttgcataatgcttatttcagaataaaaaatacaactgtactgatatggttaattatttcagGAACTTGACTATCTTGTTGGAGCTGTTGCAAACCCAAAGAAGCCATTTGCGGCCATCGTTGGTGGATCCAAGGTCTCAACTAAGATTGGGGTGATTGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA