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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATTTGATAAAATCCTCTTAGGTTTATTAAGGAGGGTTTTGGATACTAACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctacttgatctttgaaccatttctgtttgagattttctgtataattattatatattttcttctgttttcag

Basic information

species Oryza sativa
transcript LOC_Os04g59494.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 15
ACAATTTGATAAAATCCTCTTAGGTTTATTAAGGAGGGTTTTGGATACTAACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctacttg------atctttgaaccatttctgtttgagattttct--gtataattattatatattttcttctgttttcag-----------------------------------
|||||||||||| || ||| | || ||  |||| ||| | ||||||||||||||||||||||| ||||| || ||||| || |||||||| |||||||||||||   || |       ||  ||      || |   | |  |||   |  | || | ||||||  ||     |  |||| |||                                   
ACAATTTGATAAGATTCTCATGGGATTGCTAAGAAGGATATTGGATACTAACAAAAGAGTGCAAGAGGCTGCTTGTTCAGCGTTTGCAACTCTTGAAGAGgttaatgacatatatagtatgctttgttttttccccctgggaattgcataagaattagtattatgcatgcaagtaagtttgcagattctaatctgtacatattggttttctattttcag
















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|58668781|gb|CK057467.1|CK057467
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGACTTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|29626307|gb|CB631318.1|CB631318
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|29623086|gb|CB628097.1|CB628097
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58611878|gb|CK039590.1|CK039590
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58660018|gb|CK048698.1|CK048698
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58667508|gb|CK056194.1|CK056194
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTGGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58672477|gb|CK061163.1|CK061163
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58666235|gb|CK054921.1|CK054921
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58662883|gb|CK051569.1|CK051569
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|33678128|gb|CF306367.1|CF306367
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58656826|gb|CK045506.1|CK045506
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGA
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGA
EST: gi|58663523|gb|CK052209.1|CK052209
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         GAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
EST: gi|58608786|gb|CK036819.1|CK036819
EST:     ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAG                         G---CTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT
genomic: ACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctact ... ctgttttcagGAGGCTGCTGAAGAGTTAGTACCACACTTGGGAATTATTTTGCAGCACCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATTTGATAAAATCCTCTTAGGTTTATTAAGGAGGGTTTTGGATACTAACAAAAGAGTGCAGGAGGCGGCGTGTTCGGCATTTGCAACGCTTGAAGAGgttatctacttgatctttgaaccatttctgtttgagattttctgtataattattatatattttcttctgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA