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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGACGCGCGTCTTCGCGGCGTACGGGCGGGCGGGGTCGCCGCCGGCCGTGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgggagctcccccctctcctcctcctcctcctcctcctcctccgagctcccaaggaattcgaggtttggttcgccggcttgacttccggggtcgtggttgtgtggtttgtttgtttgtgctgcag

Basic information

species Oryza sativa
transcript LOC_Os07g09000.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g09000.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G146940_T01 (Zea mays), 5'ss of exon 1
GGCGACGCGCGTCTTCGCGGCGTACGGGCGGGCGGGGTCG------CCGCCGGCCG---TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgggagctcccccctctcct--cctcctcctcctcctcctcctccgagctcccaaggaattcgaggtttggttcgccggcttgacttccggggtcgtggttgtgtggtttgtttgtttgtgctgcag
             |||||||||||||| ||||||||| ||       | |||||||   | |||||||| || |||||| ||||||||||||||||||||    | |   |  || ||| |||  |||   |  ||  ||  |||  ||||||||||     | |           ||  |  |  ||   |  | || || ||  |  | |||     |                       
------------GTTCGCGGCGTACGGCCGGGCGGGGGCGGCCGGCTCCCCGGCCGCTCTCGAGGTGCTTGGCTTCGACGCCAAGGAGTGCTCCCTCTCCCCCTCTCCCCTG-
















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|58657329|gb|CK046009.1|CK046009
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58606203|gb|CK034236.1|CK034236
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|88413396|gb|CI581411.1|CI581411
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58674632|gb|CK063319.1|CK063319
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58666909|gb|CK055595.1|CK055595
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58592567|gb|CF990875.1|CF990875
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|117233168|gb|CT848021.1|CT848021
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|86904427|gb|CI308637.1|CI308637
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|87005363|gb|CI285585.1|CI285585
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|30228290|gb|CB966181.1|CB966181
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58673854|gb|CK062540.1|CK062540
EST:     TGGAGGTGCT-GG-TTCGACTCCA-GGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|86850349|gb|CI305588.1|CI305588
EST:     TGGAGGT-CTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         -CGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGC
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGC
EST: gi|58683603|gb|CK072290.1|CK072290
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58600783|gb|CK011311.1|CK011311
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGGGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58605016|gb|CK033049.1|CK033049
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|29640028|gb|CB645037.1|CB645037
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|88363482|gb|CI618043.1|CI618043
EST:     TGGAGGTGCTCGGGTTCGACTACAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58684449|gb|CK073136.1|CK073136
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58668962|gb|CK057648.1|CK057648
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|29636208|gb|CB641217.1|CB641217
EST:     TGGAGGTGCTCGGGTTCGACTCCAAAGACTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|29627838|gb|CB632849.1|CB632849
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|87005434|gb|CI285656.1|CI285656
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|88313287|gb|CI594917.1|CI594917
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTC
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTC
EST: gi|88425533|gb|CI567253.1|CI567253
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTTCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58695857|gb|CK084544.1|CK084544
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|58666737|gb|CK055423.1|CK055423
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|33796125|gb|CF323928.1|CF323928
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|88424456|gb|CI608042.1|CI608042
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
EST: gi|29674145|gb|CB670420.1|CB670420
EST:     TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTG                         GCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG
genomic: TGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACG

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: 57 (upstream exon), 19 (downstream exon)
Score: 1

GGCGACGCGCGTCTTCGCGGCGTACGGGCGGGCGGGGTCGCCGCCGGCCGTGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgg ... tgtgctgcagGCGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACGGTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGACGCGCGTCTTCGCGGCGTACGGGCGGGCGGGGTCGCCGCCGGCCGTGGAGGTGCTCGGGTTCGACTCCAAGGAGTGCTCCCTCTCCGAACCCCTGgtacgtacgggagctcccccctctcctcctcctcctcctcctcctcctccgagctcccaaggaattcgaggtttggttcgccggcttgacttccggggtcgtggttgtgtggtttgtttgtttgtgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG