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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGAACTTTCTCTCAGAAGATCTGACTACAGTAGATTAGAGAGCCAGGAGAAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgtttcttactgtaacgtttattctgtcattcctaatttgtgcatggttgttatgttcgcgttgatgtatttttcctactggtataacagaaaaa...

Basic information

species Oryza sativa
transcript LOC_Os09g36220.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36220.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G367834_T01 (Zea mays), 5'ss of exon 6
TAGAACTTTCTCTCAGAAGATCTGACTACAGTAGATTAGAGAGCCAGGAGAAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgtttcttactgtaacgtttatt--ctgtcattcctaatttgtgcatggttgttatgttcgcgttgatgtatttttcctactggtataacagaaaaa
| ||||||||||| |||||| |||||||  | | |||||||| ||| |||||||||||  |||||||||||||||| |||||||||||| |||||| |||||||||| | ||| || |  | |||  |    |  || | |   |  | |       ||||||    || |||  | | |   ||| | | |    |  |  
TGGAACTTTCTCTTAGAAGAACTGACTATGGAAAATTAGAGAACCACGAGAAAAATGATAGAAGAACACTGAACCATTCAACTTCATCTGCATTTTACTTgtaagtgctcctttctttggcttttcataatagcgatactttcgtcatcctaaaaacttatgtg-aagtagata-agtctagttacagatctggttgttatt

upper sequence: LOC_Os09g36220.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G179024_T01 (Zea mays), 5'ss of exon 6
TAGAACTTTCTCTCAGAAGATCTGACTACAGTAGATTAGAGAGCCAGGAGAAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgtttcttactgtaacgtttattctgtcattcctaatttgtgcatggttgttatgttcgcgttgatgtatttttcctactggtataacagaaaaa---
| || |||||||| |||||| |||||||| | | |||||||| ||| |||||||||||  |||||||||||||||| |||||||| ||| | |||||||||||||||   ||| || |  | |||    ||    |   ||||| || |  || | || ||    ||  |  | ||  |  || |  | |  |||        
TGGAGCTTTCTCTTAGAAGAACTGACTACGGAAAATTAGAGAACCACGAGAAAAATGATAGAAGAACACTGAACCATTCAACTTCCTCTGCGTTTTCCTTgtaagtgcacctttctttggctttt--cgtgatcctaaaaatttctgtaaagtcgataagtcta-gtacagatcttgatattatttttgtgtcagtgtttttt
















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|38471625|gb|CF955756.1|CF955756
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|29657708|gb|CB653983.1|CB653983
EST:     ACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: ACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|38479241|gb|CF963374.1|CF963374
EST:     CTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: CTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|218483797|gb|FG943383.1|FG943383
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|29645661|gb|CB650668.1|CB650668
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|58612250|gb|CK039962.1|CK039962
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|29662770|gb|CB659045.1|CB659045
EST:     AAAAATGAACGAAAAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|33798193|gb|CF324956.1|CF324956
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTC
EST: gi|58693630|gb|CK082317.1|CK082317
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|29679591|gb|CB675866.1|CB675866
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCANGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|29679636|gb|CB675911.1|CB675911
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCANGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|58694414|gb|CK083101.1|CK083101
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTG
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTG
EST: gi|29671175|gb|CB667450.1|CB667450
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|58695431|gb|CK084118.1|CK084118
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|29687696|gb|CB683971.1|CB683971
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|218491635|gb|FG966430.1|FG966430
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|66915487|gb|CX102335.1|CX102335
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
EST: gi|29659337|gb|CB655612.1|CB655612
EST:     AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTT                         GTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC
genomic: AAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGC

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: 73 (upstream exon), 71 (downstream exon)
Score: 45

TAGAACTTTCTCTCAGAAGATCTGACTACAGTAGATTAGAGAGCCAGGAGAAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgttt ... ttgttcatagGTACAACTGCAGGACAGCATCATCTACCATTAATGCTGGTGATGCTCAGGCATGCAGCACCTCGGCAACACATATAGATCTTGAAAACAAAAATGGAGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGAACTTTCTCTCAGAAGATCTGACTACAGTAGATTAGAGAGCCAGGAGAAAAATGAACGAAGAACACTGAACCACTCAACTTCATCTCCATTTTCCTTgtaagtgtttcttactgtaacgtttattctgtcattcctaatttgtgcatggttgttatgttcgcgttgatgtatttttcctactggtataacagaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC