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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatttcaaacaaatcggtgctgttttgctgactgtcagccatttccatgcatttttagcatctccagtaaaccctgacatttgtatactctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA

Basic information

species Oryza sativa
transcript LOC_Os03g15000.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G036697_T01 (Zea mays), 3'ss of exon 2
actatttcaaacaaat--cggtgctgtttt-gctgactgtcagccatttccatgcatttttagcatctccagtaaaccctgacatttgtatactctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA
 |  || || ||  ||  |   ||   ||    |  ||   | |   ||  |||      |||||| |    | |  | |   ||||  ||  | |    ||||| |||||||| ||||| |||||||||||||||||||| || || |||||||| |||||| | ||||| || ||||| || || ||||||||||| ||||
-cagttccatactgatgtctaagcaacttccattttcttggaactgatttaatgttgcagtagcatatgtgctga--cattttatttccatcttttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGCCCCATCTGCAGGCAGCCTGTGGAGCGTCTCCTGGAGATCAAAGTGAACA

upper sequence: LOC_Os03g15000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G426140_T01 (Zea mays), 3'ss of exon 14
actatttcaaacaaatcggtgctgttttgctgactgtcagccatttccatgcatttttagcatctccagtaaaccctgacattt-gtatac---tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA
     | |  |    |        ||    |  ||   | |   ||    |     ||||||| |    ||||||||||||||| |  |||   |    | ||||| |||||||| ||||| |||||||||||||||||||| || || |||||||| |||||| | ||||| |||||||| || || ||||||||||| ||||
----atactgatgtcttaagcaacttccattttctcagaactgatttagcgttgaattagcatatgtgctaaaccctgacattttgcttacatcttcactgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGCCCCATCTGCAGGCAGCCTGTTGAGCGTCTCCTCGAGATCAAAGTGAACA

upper sequence: LOC_Os03g15000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G860152_T02 (Zea mays), 3'ss of exon 2
actatttcaaacaaatcggtgctgttttgctgactgtcagccatttccatgcatttttagcatctccagtaaaccctgacattt-gtatac---tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA
     | |  |    |        ||    |  ||   | |   ||    |     ||||||| |    ||||||||||||||| |  |||   |    ||||||| |||||||| ||||| |||||||||||||||||||| || || |||||||| |||||| | ||||| |||||||| || || ||||||||||| ||||
----atactgatgtcttaagcaacttccattttctcagaactgatttagcgttgcattagcatatgtgctaaaccctgacattttgcttacatcttcactacagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGCCCCATCTGCAGGCAGCCTGTTGAGCGTCTCCTCGAGATCAAAGTGAACA

upper sequence: LOC_Os03g15000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g02970.t01 (Vitis vinifera), 3'ss of exon 3
actatttcaaacaaatcggtgctgttttgctgactgtcagccatttccatgcatttttagcatctccagtaaaccctgacatt-tgtatact-ctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA
 | || | |  |  |  | |  |         | |||    |||||   |   || |    |  |   |        ||  || | |  |||  |||| |||||||||||  | | ||||||||||||  |||||| ||||| || ||| ||||| || |||||||| || ||||||| ||| || |||||||| || ||||
tcaatcttatgctta--gattttaaagcttaaattgttgaacattttagtttcttgtgtctaattatgggttggttggattttgtttggactattggtgcagTGTATGTGTGGTGGGTGTGCCAAGGTTTTGAGGTTCCAGATGAACCGATGCCCTATTTGCCGACAACCAGTTGAGCAGCTCCTAGAGATCAAGGTAAACA

upper sequence: LOC_Os03g15000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ16057 (Selaginella moellendorffii), 3'ss of exon 2
actatttcaaacaaatcggtgctgttttgctgactgtcagccatttccatgcatttttagcatctccagtaaaccctgacatttgtatactctggt-acagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA
                                   ||  ||    |  ||  | || | |  |    ||       |    ||| | |  |||  |  ||||||||||| |||||||| ||||| || ||||||| |||||||| ||| |||||||| ||  |    || || ||||| || || |||||||| ||    |
-----------------------------------gtaggctggct--atatacttctggttttcatagctctttttttttttttttttttcttcttgcagTGTATGTGTAGCGAGTGCGCCAAAGTGCTGAGGTTCCAGACGAACCGCTGCCCGATTTGTAGGTGCCCTGTGGAGCGACTGCTCGAGATCAAGGTTCCAA

upper sequence: LOC_Os03g15000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ16938 (Selaginella moellendorffii), 3'ss of exon 2
actatttcaaacaaatcggtgctgttttgctgactgtcagccatttccatgcatttttagcatctccagtaaaccctgacatttgtatactctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA
                    |  |  | |||   | |      ||| ||| |  |  |||  | |    |   | ||  |  |      |||   | ||||||||||| |||||||| ||||| || ||||||| |||||||| ||| |||||||| ||  |    || || ||||| || || |||||||| ||    |
--------------------gtaggctggctatatatttctggttttcat-cgctcatagttttttttttt--ctctctctctctctctctcgtttgcagTGTATGTGTAGCGAGTGCGCCAAAGTGCTGAGGTTCCAGACGAACCGCTGCCCGATTTGTAGGTGCCCGGTGGAGCGACTGCTCGAGATCAAGGTTCCGA

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|86828499|gb|CI278607.1|CI278607
EST:     TCCCATGTAGGCATATG                         TGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
genomic: TCCCATGTAGGCATATGgtaagtatcc ... tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
EST: gi|86859202|gb|CI277093.1|CI277093
EST:     TTGCCTCTCGGAGCCAAGGGATAACTACCGTTCTCCCATGTAGGCATATG                         TGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
genomic: TTGCCTCTCGGAGCCAAGGGAT-ACTACCGTTCTCCCATGTAGGCATATGgtaagtatcc ... tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
EST: gi|86855802|gb|CI271021.1|CI271021
EST:     TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATG                         TGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
genomic: TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATGgtaagtatcc ... tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
EST: gi|218498901|gb|FG944514.1|FG944514
EST:     TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATG                         TGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGAACCGGTGC
genomic: TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATGgtaagtatcc ... tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
EST: gi|218501166|gb|FG964612.1|FG964612
EST:     TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATG                         TGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
genomic: TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATGgtaagtatcc ... tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
EST: gi|86499438|gb|CI142071.1|CI142071
EST:     TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATG                         TGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
genomic: TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATGgtaagtatcc ... tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
EST: gi|58663479|gb|CK052165.1|CK052165
EST:     TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATG                         TGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC
genomic: TTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATGgtaagtatcc ... tctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatgcatttttagcatctccagtaaaccctgacatttgtatactctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA
                            ccctgac  putative branch site (score: 3)
                                   atttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatttcaaacaaatcggtgctgttttgctgactgtcagccatttccatgcatttttagcatctccagtaaaccctgacatttgtatactctggtacagTGTATGTGCAGCGAGTGTGCCAAGGTCCTGAGGTACCAGACGACCCGGTGCCCGATCTGCCGACAGCCCGTTGAGCGGCTACTTGAGATCAAAGTCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA