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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttgtcgcacacatattgcatttagctaagcaggagaggtatggttagtcacttgtcttcattttgattctgtatgctctctaaacgtgttgctgccatctttcttacatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCAAATCTTAAGGCACAGCTTTTTAACATGCCATTTGGATATATCTTGACAC

Basic information

species Oryza sativa
transcript LOC_Os06g47350.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47350.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G415846_T02 (Zea mays), 3'ss of exon 11
gttagttttgtcgcacacatattgcatttagctaagcaggagaggta--tggttagtcacttgtcttcattt---tgattctgtatgctctcta--aacgtgttgctgccatctttcttacatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCAAATCTTAAGGCACAGCTTTTTAACATGCCATTTGGATATATCTTGACAC
||| ||| || |  |  |       ||||| ||||||| |||| | |  |||| |    | |||  |   |         ||||      ||||  | | | |   | |  | ||| ||| | |||||||| || |||||  |||| |||||||| ||||||||||||||||||||||||||||||||   ||| ||||||   |||| | |  |  ||||||||   |
gtttgttatgccatattctctgcatatttaactaagcaagagaagaagttggtcaaatgcatgttattgctcaaccacccctgttcctgttctagcatcatatgctttctgtgtttttta-acctgcagGCTGTGATGTATGTCCTATGCTTTCGGTTAAGATCTATTATGGACTACCCAAATCTTAAACAACAACTTTTTCGAATGCGAATCCGGGATATCTTGGTCC
















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|2799623|gb|AA752612.1|AA752612
EST:     AAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: AAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
EST: gi|58668152|gb|CK056838.1|CK056838
EST:     GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
EST: gi|218504600|gb|FG967431.1|FG967431
EST:     GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
EST: gi|33812524|gb|CF332150.1|CF332150
EST:     GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTA
genomic: GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTA
EST: gi|66922574|gb|CX109422.1|CX109422
EST:     GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
EST: gi|29628119|gb|CB633130.1|CB633130
EST:     GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAN                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
EST: gi|58668829|gb|CK057515.1|CK057515
EST:     GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
EST: gi|58680790|gb|CK069477.1|CK069477
EST:     GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
EST: gi|56158395|gb|AU075492.2|AU075492
EST:     AAATCATC-AAT-NTTTACGCAAGCTGTCA-                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: AAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
EST: gi|218492292|gb|FG954140.1|FG954140
EST:     GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG                         GCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA
genomic: GGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAGgttagttttg ... acatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgattctgtatgctctctaaacgtgttgctgccatctttcttacatctgcagGCAGTCATGTACATCCTGTGCTTTCGCTTAAGATCTATTATGGACTACCCAAATCTTAAGGCACAGCTTTTTAACATGCCATTTGGATATATCTTGACAC
                                        ttcttac  putative branch site (score: 2)
                                     tctttcttacatct  CT-rich tract
                                       tttctta  TA-rich tract