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'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccgtttgttgcttattgtcattgcttttgatttgatcctatgatgcttccttttacactgcatggaaaactctcagatactaacttggttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAAGCCTCGGAGATTCAAAACTTTCGTAGAAGCATTG

Basic information

species Oryza sativa
transcript LOC_Os03g13790.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G085427_T02 (Zea mays), 3'ss of exon 5
-----taccgtttgttgcttattg-tcattgcttttgatttgatcctatgatgcttccttttacactgcatggaaaactctcagatactaacttggttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAAGCCTCGGAGATTCAAAACTTTCGTAGAAGCATTG
     || | ||||| |        | | |  |    | ||  |   | |||| | | |  |  ||||| ||| |     |   ||| ||  | | ||| ||| ||||||||||||||||| ||||||||||||| |||||||||  ||||||| || |||||||| |||||||| || ||||||||| ||
caacttagcttttgtagaaagcgaataaataatgacaacttcgtttaaggatg-tgcttgctcgactgc-tggcag----ttcaatattagttggttttgatgtagGTGGTCTCTGCTTGAGAAATTTAGCTGCACTGCATCAAAGTTGCATCTCAAACCTCGGAGGTTCAAAACATTTGTAGAAGCACTG

upper sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 5
-----taccgtttgttgcttatt-gtcattgcttttgatttgatcctatgatgcttccttttacactgcatggaaaactctcagatactaacttggttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAAGCCTCGGAGATTCAAAACTTTCGTAGAAGCATTG
     || | ||||| |       || | |  |     |||  |   | |||        | | | ||| ||| |     |   ||| || || | ||| ||||||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||||||||| |||||||| || ||||||||||||
taacttagcttttgtagaaggcgagtaaataatggcagtttcgtttaaggatatgcttgctca-attgc-tggcag----ttcaatattagctggttttgatgcagGTGGTCTCTGCTTGAGAAATTTAGCTGCAGTGCATCAAAGCTGCACCTGAAGCCTCGGAGGTTCAAAACATTTGTAGAAGCATTG

upper sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G36960.3 (Arabidopsis thaliana), 3'ss of exon 5
taccgtttgttgcttattgtcattgcttttgatttgatcctatgatgcttccttttacactgcatggaaaactctcagatactaacttg-gttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAAGCCTCGGAGATTCAAAACTTTCGTAGAAGCATTG
|      |  | ||   || |||   ||   || | ||  | | |   |  |  | |    |  ||   ||     | || ||   |   || |  |||||||||||| |||||||||| | ||||||||  || |||||||| ||||| ||||| ||||||||||||   ||  |||| || |||
tcttccattctcctagatgacatgatttcacatatcatgatctta-attatcactcagctcgtctgactaaagtaaacatgctttttcatgtgtcttgcagGTGGTCTTTGCTTGAAAAGTATAGCTGCAAAGCTTCAAAACTTCATCTCAAGCCCCGGAGATTCAAACTATTTATAGAGGCCTTG

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|117217875|gb|CT845173.1|CT845173
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|29628330|gb|CB633341.1|CB633341
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|88373410|gb|CI614746.1|CI614746
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTATCTGCTTGAAAAATTTAGCTGCAGT
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGT
EST: gi|88351778|gb|CI617503.1|CI617503
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTT
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTT
EST: gi|58689184|gb|CK077871.1|CK077871
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|88352611|gb|CI624550.1|CI624550
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAA
EST: gi|29621639|gb|CB626650.1|CB626650
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|29630702|gb|CB635711.1|CB635711
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|58612137|gb|CK039849.1|CK039849
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|58666001|gb|CK054687.1|CK054687
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|29618831|gb|CB623843.1|CB623843
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|88337044|gb|CI628130.1|CI628130
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|29617184|gb|CB622196.1|CB622196
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCTAAACTGCATCTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAA
EST: gi|88412252|gb|CI573528.1|CI573528
EST:     TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTG                         GTGGTCTCTGCTTGAA
genomic: TCGCTCGATGCAAAAAATTCCAAGGACACCATTGCTGCTATGCTCTGCTGgtaattaaat ... ttttatgcagGTGGTCTCTGCTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttccttttacactgcatggaaaactctcagatactaacttggttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAAGCCTCGGAGATTCAAAACTTTCGTAGAAGCATTG
                                  tactaac  putative branch site (score: 0)
                                             ttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccgtttgttgcttattgtcattgcttttgatttgatcctatgatgcttccttttacactgcatggaaaactctcagatactaacttggttttatgcagGTGGTCTCTGCTTGAAAAATTTAGCTGCAGTGCATCAAAACTGCATCTGAAGCCTCGGAGATTCAAAACTTTCGTAGAAGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - -tgttgct
- - - - - - - - - - - -tgctttt
- - - - - - - - - - - - - - - - - - - - tatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgga