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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_Os04g41100.3
intron # 3
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|58687429|gb|CK076116.1|CK076116
EST:     CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAG                         ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
genomic: CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAGgtatttcgtt ... tttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
EST: gi|29679248|gb|CB675523.1|CB675523
EST:     CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAG                         ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC
genomic: CCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAGgtatttcgtt ... tttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 47 (downstream exon)
Score: 42

TACCGCCATTGATATGTGGTCTGTGGGCTGCATAATGGCAGAGCTTTTGGCCAAAGAACCATTATTTAATGGGAAAACTGAGTTTGAACAGCTAGATAAGgtatttcgtt ... tttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgatatatattatatttgatcatatctcatggtgaagctacttttattgcagATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC
                atttgat  putative branch site (score: 42)
                                        ctactttt  putative PPT
     atatatattatatttg  TA-rich tract