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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcgtttgacttgtgattttgcatccttgcaattactatatttttttcagaggtctcatgttggatttcctttcctgttgcagatacctataaaccttgatatatattatatttgatcatatctcatggtgaagctacttttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC

Basic information

species Oryza sativa
transcript LOC_Os04g41100.6
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G179097_T02 (Zea mays), 3'ss of exon 3
gtatttcgtttgacttgtgattttgcatccttgcaattactatatttttttcagaggtctcatgttggatttcctttcctgttgcagatacctataaaccttgatatatattatatttgatcatatctcatggtgaagctacttttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC
                                                              | ||  |||| || |    |   |  | |||  |   ||||||||| |   |  | ||| |||||||||| ||||||||||| | | |||||| ||||||||||| ||||||||||| |||||||| |||||||||||||| ||||| || ||||| ||||| |||||||| ||||||||
-------------------------------------------------------------gtatttaatttgctctgaactccta--ttcctgcagctcttgatataaacatttatcgatgatatctcatgttgaagctacttctttggcagATTTTTAGAACACTCGGCACACCTAATGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGTGTGAAAGTAAATTTTGTTAAACAACC

upper sequence: LOC_Os04g41100.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 3
gtatttcgtttgacttgtgattttgcatccttgcaattactatatttttttcagaggtctcatgttggatttcctttcctgttgcagatacctataaaccttgatatatattatatttgatcatatctcatggtgaagctacttttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC
                                                             |||     |   ||   || ||    ||  ||  |   ||||||||| | | |  ||||| |||||||||| ||||||||||| | | |||||| |||||||||||||||||||||| ||||||||| |||||||||||||| ||||| || || || ||||| |||||||||||||||||
-----------------------------------------------------------gtatgcaaattgctctgaactctt----atttctgcaggtcttgatataaacttttgttgatgatatctcatgttgaagctacttctttggcagATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGCGTGAAAGTAAATTTTGTCAAACAACC
















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|218494622|gb|FG958132.1|FG958132
EST:     CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGC----T-AG                         ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
genomic: CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAGgtatttcgtt ... tttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
EST: gi|29640024|gb|CB645033.1|CB645033
EST:     CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAG                         ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
genomic: CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAGgtatttcgtt ... tttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
EST: gi|29672610|gb|CB668885.1|CB668885
EST:     CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAG                         ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
genomic: CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAGgtatttcgtt ... tttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
EST: gi|58687429|gb|CK076116.1|CK076116
EST:     CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAG                         ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
genomic: CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAGgtatttcgtt ... tttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
EST: gi|29679248|gb|CB675523.1|CB675523
EST:     CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAG                         ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
genomic: CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAGgtatttcgtt ... tttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgatatatattatatttgatcatatctcatggtgaagctacttttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC
                atttgat  putative branch site (score: 5)
                                        ctactttt  putative PPT
     atatatattatatttg  TA-rich tract