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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGGCACCGCCGCCGGAGCTCCTCCCTGCTCCCTCTACTGGGTTGGCGGGGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgccctagctcttccctgggatcgatttcgctcctgatctagttcgttctggtctccgctgtgaatttcaggaaatctgttccaaatataggtgttt...

Basic information

species Oryza sativa
transcript LOC_Os01g59600.1
intron # 1
splice site 5'
intron type U2

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|33692105|gb|CF320344.1|CF320344
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT---                         -A--AGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|218484300|gb|FG947697.1|FG947697
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|2442684|gb|C74455.1|C74455
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|84117381|gb|CD151148.1|CD151148
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88391006|gb|CI592914.1|CI592914
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|163919763|gb|EG714885.1|EG714885
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|58601557|gb|CK012085.1|CK012085
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|12622988|gb|AU173201.1|AU173201
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|58602516|gb|CK013044.1|CK013044
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88407414|gb|CI583872.1|CI583872
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88739654|gb|CI763162.1|CI763162
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88423678|gb|CI617030.1|CI617030
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|33657519|gb|CF280133.1|CF280133
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|29668731|gb|CB665006.1|CB665006
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|44665861|gb|CR279295.1|CR279295
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88391292|gb|CI595546.1|CI595546
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|87017761|gb|CI289894.1|CI289894
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88300705|gb|CI589697.1|CI589697
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|218496122|gb|FG967266.1|FG967266
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88400550|gb|CI595971.1|CI595971
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88738269|gb|CI761777.1|CI761777
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACCAGGATAC
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCAC-AGGATAC
EST: gi|88425566|gb|CI569290.1|CI569290
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88722475|gb|CI745985.1|CI745985
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|33686423|gb|CF314662.1|CF314662
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88393093|gb|CI616577.1|CI616577
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTACATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88343491|gb|CI621859.1|CI621859
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|2428359|gb|C72822.1|C72822
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88454340|gb|CI569912.1|CI569912
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88722486|gb|CI745996.1|CI745996
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|87008998|gb|CI304941.1|CI304941
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|66913113|gb|CX099961.1|CX099961
EST:     GGAGTGGATCGGGGATCTGCACGCAAGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAAAATAGTTGAAGATGAACAACATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88396858|gb|CI578007.1|CI578007
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGT---                         -A--AGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88718828|gb|CI742338.1|CI742338
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88727129|gb|CI750784.1|CI750784
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88763617|gb|CI773064.1|CI773064
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|88420790|gb|CI564626.1|CI564626
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|569795|gb|D40644.1|D40644
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
EST: gi|33686716|gb|CF314955.1|CF314955
EST:     GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAG                         GAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG
genomic: GGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACG

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: 65 (upstream exon), 71 (downstream exon)
Score: 103

GTCGGCACCGCCGCCGGAGCTCCTCCCTGCTCCCTCTACTGGGTTGGCGGGGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgcccta ... ttttcttcagGAGTAGATAACACAGAATAGTTGAAGATGAGCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGGCACCGCCGCCGGAGCTCCTCCCTGCTCCCTCTACTGGGTTGGCGGGGAGTGGATCGGGGATCTGCACGCAGGGGCCGATTTCTTCTCTTCGTAAGgtatgccctagctcttccctgggatcgatttcgctcctgatctagttcgttctggtctccgctgtgaatttcaggaaatctgttccaaatataggtgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA