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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaacttttcatgctctgaactcgtaagtgaatttaagttacaacttgatatggtttgcacatcaacttgcgtaccatgccgatttgcattctcgcaagagattcttgcatgtgtgtgacatgtgaaatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCGGTTATAAAATCAGCATTGACATGGAAAGGTTTAACTTCTCTGCTAAGAA

Basic information

species Oryza sativa
transcript LOC_Os02g47310.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G035213_T01 (Zea mays), 3'ss of exon 4
gtaaaaaaacttttcatgctctgaactcgtaagtgaatttaagttacaacttgatatggtttgcacatcaacttgcgtaccatgccgatttgcattctcgcaagagattcttgcatgtgtgtgacatgtgaaatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCGGTTATAAAATCAGCATTGACATGGAAAGGTTTAACTTCTCTGCTAAGAA
                        ||   | || |     |     |||  ||  |   |||||         || ||   ||  ||||    | |     |   |||||||     ||| || ||||||    || ||||||||| | ||||||||| ||||| |||||||| ||||| || ||||| || || |||||||||||  | |||||||| || || || |||||||| |  |
----------------------ccacctattagcggg---acacaccaaactggca--atttgcctgc-----tgtgtgtgatatcgatacaaaata----acaggattcttttcgctgtttg-catgtg----gtcccagGATATCAAGACAGCTGACTGGTCGGAGAACGTGGCCCCGTTTTGGCCCGCCGTGATAAAATCAGCGCTAACATGGAAGGGCTTCACCTCTCTGCTGACGA

upper sequence: LOC_Os02g47310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaaaaaacttttcatgctctgaactcgtaagtgaatttaagttacaacttgatatggtttgcacatcaacttgcgtaccatgccgatttgcattctcgcaagagattcttgcatgtgtgtgacatgtgaaatgtgc-----cagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCGGTTATAAAATCAGCATTGACATGGAAAGGTTTAACTTCTCTGCTAAGAA
                                                          |||   | ||   ||  | |    ||||||      | ||         || ||  |      |   || |||||| ||       ||||||| | |   || ||||||||||||||||| || || ||||||||||||||||||    | ||||| |||||||| ||  |    ||||||||  | |
----------------------------------------------------------gttattatattccctaccctttgctgccgaaaacattacttaactagagtttttttactaaactagaatctgaaatatgtgtttttagGATATTAAGTGTGCGGATTGGTCAGAGAACGTAGCTCCTTTCTGGCCTGCGGTTATACGGACTGCATTAACATGGAAGGGCCTTGTGTCTCTGCTTCGTA
















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|86252110|gb|CI055847.1|CI055847
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|117221355|gb|CT858945.1|CT858945
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|86502638|gb|CI145271.1|CI145271
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|86874770|gb|CI325281.1|CI325281
EST:     CTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACACCTGATTGGTCAGAGAACGTCCCCCCATTCTGGCCTGCG
genomic: CTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|88217321|gb|CI217170.1|CI217170
EST:     GGTGCTCTCCTTCTGATTATGTCAGAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|88982830|gb|CI028243.1|CI028243
EST:     GGTGCTCTCCTTCTGATTATGTCGAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|86848935|gb|CI295738.1|CI295738
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|38477974|gb|CF962107.1|CF962107
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|88257977|gb|CI360563.1|CI360563
EST:     ATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAACTGATTGGTCAGAGAACCTCGCCCCATTCTGGCCTCCG
genomic: ATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|88264967|gb|CI368741.1|CI368741
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|88965269|gb|CI009305.1|CI009305
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|86480720|gb|CI123353.1|CI123353
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|29675076|gb|CB671351.1|CB671351
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|29643991|gb|CB648998.1|CB648998
EST:     GGTGCTCTCCTTCTGAGTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGGTGATTGGTCAGAGAACGTCGCCCCATTCTGCCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|86594355|gb|CI251227.1|CI251227
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
EST: gi|38469736|gb|CF953867.1|CF953867
EST:     GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAG                         GATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG
genomic: GGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCG

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), 72 (downstream exon)
Score: 43

TGAGCTGAATCTCCTGAAAAGGATATGCGATGCATATTATCTCCCAGACTGGTGCTCTCCTTCTGATTATGTCAAAATTGCCGAGTCACTGTCTCTTGAGgtaaaaaaac ... aatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCGGTTATAAAATCAGCATTGACATGGAAAGGTTTAACTTCTCTGCTAAGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaaacttttcatgctctgaactcgtaagtgaatttaagttacaacttgatatggtttgcacatcaacttgcgtaccatgccgatttgcattctcgcaagagattcttgcatgtgtgtgacatgtgaaatgtgccagGATATAAGGACAGCTGATTGGTCAGAGAACGTCGCCCCATTCTGGCCTGCGGTTATAAAATCAGCATTGACATGGAAAGGTTTAACTTCTCTGCTAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA