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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgtatctagctcaacttgttctggtatcatctggatgcacttcagtttcagtattgctaatgaatggcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGCAACGTCCATGGTGTAAATCCAAAGTTCCTTAAGATTGGAGATAAAATAA

Basic information

species Oryza sativa
transcript LOC_Os02g33580.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
gtgctgtatctagctcaacttgttctggta-tcatctggatgcacttcagtttcagtattgctaatgaatggcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGCAACGTCCATGGTGTAAATCCAAAGTTCCTTAAGATTGGAGATAAAATAA
|| || | | ||||| |  ||||| || || | |   |||||| | | |       || || || | |      | |  |||| |||||||| |||||||||||||| ||| | || ||||||||| ||||||| || |||||||| || ||||||||||| |||||||||||  ||||||
gtactttgtatagcttag-ttgttttgttaattacacggatgcccatgaacactcctaatgttattca------tctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA

upper sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G11670.2 (Arabidopsis thaliana), 3'ss of exon 5
---------gtgctgtatctagctcaac-ttgttctggtatcatctggatgcacttcagtt-tcagtatt------gctaatgaatggcttatgc-------agGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGCAACGTCCATGGTGTAAATCCAAAGTTCCTTAAGATTGGAGATAAAATAA
          | || ||| |     | | ||||||||   |    || || | ||| | |  | | || |      ||||||  ||   || | |       ||||| | || || ||||| ||||| || ||| | || |||||| || | ||||| ||||||||||| ||||| |||||||||| |||||| || |||||  
gtgaatcatctactctatttcttcaagccttgttctg---ttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
















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|29678872|gb|CB675147.1|CB675147
EST:     TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAG                         GTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
genomic: TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
EST: gi|29678870|gb|CB675145.1|CB675145
EST:     TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAG                         GTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
genomic: TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
EST: gi|29640793|gb|CB645800.1|CB645800
EST:     TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAG                         GTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
genomic: TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
EST: gi|25798230|gb|CA754191.1|CA754191
EST:     TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAG                         GTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
genomic: TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
EST: gi|116875217|gb|EC365725.1|EC365725
EST:     TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAG                         GTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
genomic: TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
EST: gi|11442630|gb|BF430533.1|BF430533
EST:     TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAG                         GTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
genomic: TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
EST: gi|218500847|gb|FG954980.1|FG954980
EST:     TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAG                         GTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
genomic: TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGC
EST: gi|29640227|gb|CB645236.1|CB645236
EST:     TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAG                         GTTTTACGTCTGTCTG
genomic: TCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTG

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: 71 (upstream exon), 75 (downstream exon)
Score: 19

GAATTACCTAGAATATATCAAGAGAGAGAAGAATGGTGCTCTTCAAGCTTTCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatc ... gcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGCAACGTCCATGGTGTAAATCCAAAGTTCCTTAAGATTGGAGATAAAATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtatcatctggatgcacttcagtttcagtattgctaatgaatggcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGCAACGTCCATGGTGTAAATCCAAAGTTCCTTAAGATTGGAGATAAAATAA
                                 tgctaat  putative branch site (score: 19)
                                    taatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgtatctagctcaacttgttctggtatcatctggatgcacttcagtttcagtattgctaatgaatggcttatgcagGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGCAACGTCCATGGTGTAAATCCAAAGTTCCTTAAGATTGGAGATAAAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT