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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgagacggacatcttgcattgcttaaatttggtgcatcaatcaactataccctgtaacagataaacagttaatcttgcattccggtgaactggtagtcactttttcttaatgtaaatatgcaattattgcttctgaattcatagaagcttttcatatag

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G119725_T02 (Zea mays), 5'ss of exon 6
GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactga--gacggacatcttgcattgcttaaatttggtgcatcaatcaactataccctgtaacagataaacagttaatcttgcattccggt-gaactggtagtcactttttcttaatgtaaatatgcaattattgcttctgaattcatagaagcttttcatatag
||||| | |||||| ||  |||| |||||||||||||| ||||| |||   || ||||| ||||||||||| || |||| ||||||||||||  ||| | || ||| |  | |||||  |  ||| ||||| |  ||  || |||  || |||  |||||  |||   |||   | |  |||| ||||||||||| | || |  | |  ||| | |  || ||||  | ||||   ||| || |  |||||
GACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGGCAAAAGGCAAATATTGATGCAGCGGTCAGAAAGgtaactgacagactggcaccttac-ctacttaagctcagtgtatcaaacttctgaactctgggactgatgtacagtagatcc-acatcgtgattaaacttgtagtcactttat-ttgaaatgagcatgtagtcctttcttccaatttcacgtaagtttcttttatag

upper sequence: LOC_Os02g19510.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G006507_T02 (Zea mays), 5'ss of exon 6
GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactg--agacggacatcttgcattgcttaaatttggtgcatcaatcaactataccctgtaacagataaacagttaatcttgcattccggt-gaactggtagtcactttttcttaatgtaaatatgcaattattgcttctgaattcatagaagcttttcatatag
||||| | |||||| ||  |||| |||||||| ||||| ||||| |||   || ||||| ||||||||||| || ||||||||||||||||  |||| | |||||| |  |||||||  |||||||| ||| |  ||   |  ||  || |||  ||| |  |||| ||||   | |  |||| ||||||||||| | || |  | |  ||||| |     || |  | |||||  | | || |  |||||
GACCTTACTAGCGAGCCGAGGTATCTTGTTACATTTACTGTTGGTATTGGGCAAAAGGCAAATATTGATGCAGCAGTCAAAAAGgtaactggcagactgccatcttac-ctgcttaaccttggtgcaccaaacttctgagctttgggactgatgtacactagatct-gcatcgtgattaaacttgtagtcactttat-ttgaaatgagcatgcagtc----ctaccaatttcatgtatgtttcttttatag
















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|428327|gb|D24475.1|D24475
EST:     TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAG                         TTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
EST: gi|88360895|gb|CI625201.1|CI625201
EST:     TTACAGTTGGAATTACTCAGAAGGCTAATATTGATGCTGCTGTCAAAAAG                         TTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
EST: gi|428279|gb|D24427.1|D24427
EST:     TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAG                         TTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
EST: gi|428340|gb|D24488.1|D24488
EST:     TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAG                         TTTTCAGATAAATTCACTATCA
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCA
EST: gi|29673248|gb|CB669523.1|CB669523
EST:     TTACAGTTGGAATTACACAGAACGCTAATATTGATGCTGCTGTCAAAAAG                         TCT-CAGATAAAT-CACTATCATGCTAT
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTAT
EST: gi|29676038|gb|CB672313.1|CB672313
EST:     TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAA-G                         TTTTCAGATAA-TTCACTATCATGCTAT
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTAT
EST: gi|29640936|gb|CB645943.1|CB645943
EST:     TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAG                         TTTTCAGATAAATTCACTATCATGCTATTCCATTATGA
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGA
EST: gi|66913022|gb|CX099870.1|CX099870
EST:     TTACAGTTGGAATTACACAGAAGGTTAATATTGATGCTGCTGTCAAAAAG                         TTTTCAGATAAATTCACTATCATGCTATTTCATTATGA
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGA
EST: gi|33675555|gb|CF303794.1|CF303794
EST:     TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAG                         TTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
genomic: TTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
EST: gi|86906524|gb|CI294647.1|CI294647
EST:     TGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAG                         TTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT
genomic: TGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACT

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: 62 (upstream exon), 75 (downstream exon)
Score: 36

GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgaga ... tttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACTGAATGGGATGAATTTGAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAGgtaactgagacggacatcttgcattgcttaaatttggtgcatcaatcaactataccctgtaacagataaacagttaatcttgcattccggtgaactggtagtcactttttcttaatgtaaatatgcaattattgcttctgaattcatagaagcttttcatatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT