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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC

Basic information

species Oryza sativa
transcript LOC_Os03g52630.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
gtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
||||    || ||    |  ||| | | ||   |||   |||||||||| ||    |||  |  |      ||| |   || |||||||||| || ||  |||| || ||||||||| ||||||||||||||||||||||||| |||||||||||||| |||||| |||| ||||||||||| || || |
gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaa-agtgggtcggtagttaaaatctgctcgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G110735_T01 (Zea mays), 3'ss of exon 5
gtaag-gttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
||||  |  |||||    |||||||  ||||   ||| | |||    |   |||    |  ||     |   ||| |  || |||||||||||||| ||  |||| || ||||||||| ||||||||||||||||||||||||| |||||||||||||| |||||| ||||||||||||| || || || |
gtaaaagcattgttcttaatgctctcaaagtgcccaacg-tacg---gggaagtgaaattgatagttaaattaaatctgttaaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCATCACAGAGGCGCGTCGATAC

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ31524 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
                                                       | |    ||        ||    ||   | | ||| | || ||  | || || |||||||||| | | ||||||||||||||||| || || |||||||| ||||||  ||  || ||| |||  |||||  | |
-------------------------------------------------------gttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTC

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|58670607|gb|CK059293.1|CK059293
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATG
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATG
EST: gi|2280737|gb|C25232.1|C25232
EST:     ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|27576324|gb|CA999018.1|CA999018
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGT
EST: gi|29639819|gb|CB644828.1|CB644828
EST:     ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29674436|gb|CB670711.1|CB670711
EST:     CACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: CACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29624498|gb|CB629509.1|CB629509
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29639818|gb|CB644827.1|CB644827
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|58663082|gb|CK051768.1|CK051768
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29629441|gb|CB634450.1|CB634450
EST:     ACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|27578175|gb|CB000870.1|CB000870
EST:     CTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: CTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|38469334|gb|CF953465.1|CF953465
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29629254|gb|CB634265.1|CB634265
EST:     GTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCTTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|396941140|gb|HO188349.1|HO188349
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29623193|gb|CB628204.1|CB628204
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29643849|gb|CB648856.1|CB648856
EST:     ACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29630277|gb|CB635286.1|CB635286
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29673808|gb|CB670083.1|CB670083
EST:     GCAAATTTGCAAGGTCACAG                         CTCGATTATGTCTTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|163926677|gb|EG713693.1|EG713693
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29668386|gb|CB664661.1|CB664661
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
                         atttgac  putative branch site (score: 4)
                                        cccttc  putative PPT
                                           ttcaattt  TA-rich tract