Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACATGCTAATCGACCAGCATATTCATCATTGGAGAGAGTGATACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctctatctttttcttcatctcacgatcaatcatgattctgtacggctgcatcgtatcttgttgaacatctttttttttgttcttatctatctt...

Basic information

species Oryza sativa
transcript LOC_Os01g56820.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56820.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G085602_T02 (Zea mays), 5'ss of exon 6
CACATGCTAATCGACCAGCATATTCATCATTGGAGAGAGTGATACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaa-catctctatctttttcttcatctcacgatcaatcatg--attctgtacggctgcatcgtatcttgt--tgaacatctttttttttgttcttatctatctt
||||||||||||  |||||||||||||| |||||||| ||| | |||||||| |||||||||||||||||||||||||||||||||||||||||||  ||| | |  |   |  ||| |  | | |  |  ||   ||  |||  |  |   | |||  ||||  | |   | |  | |  |||  | ||       
CACATGCTAATCTTCCAGCATATTCATCGTTGGAGAGGGTGGTCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcgcaaagtaacttgtcagcgaatggttcagtatcgtatcttgttagtttcacttgtagtttgtgctcattgtgtaatgtcctgtggtgatgc-----
















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|86834565|gb|CI344496.1|CI344496
EST:     CAGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: CAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
EST: gi|88260325|gb|CI362618.1|CI362618
EST:     TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
EST: gi|89177839|gb|CI391018.1|CI391018
EST:     CAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGGCAAG                         GATTGTTACCCCCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGGTG
genomic: CAACTGTGGTTAGACAATACCTACAGCAGGAAGTT-GGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAA-GGTG
EST: gi|88413765|gb|CI528537.1|CI528537
EST:     TACAGCAAGCAACTGTGGTTAGACAATACCTACGGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
EST: gi|58695745|gb|CK084432.1|CK084432
EST:     TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
EST: gi|88965704|gb|CI006600.1|CI006600
EST:     TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
EST: gi|117234957|gb|CT847981.1|CT847981
EST:     TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
EST: gi|88465467|gb|CI520019.1|CI520019
EST:     TACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: TACCTACAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
EST: gi|88215238|gb|CI215087.1|CI215087
EST:     TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
EST: gi|88413879|gb|CI528651.1|CI528651
EST:     TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA
genomic: TACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctc ... cttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAGGTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACATGCTAATCGACCAGCATATTCATCATTGGAGAGAGTGATACAGCAAGCAACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaacatctctatctttttcttcatctcacgatcaatcatgattctgtacggctgcatcgtatcttgttgaacatctttttttttgttcttatctatctt

- - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGCAA