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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaatttatctacttttcttctcaccatgaagttatctctctagtccccgactaacagttcaataaaaactag

Basic information

species Oryza sativa
transcript LOC_Os02g45070.2
intron # 18
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|38471881|gb|CF956012.1|CF956012
EST:     AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATC
genomic: AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATC
EST: gi|218479705|gb|FG950878.1|FG950878
EST:     AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCNTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|58673688|gb|CK062374.1|CK062374
EST:     AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|14571449|gb|BI118817.1|BI118817
EST:     AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|38469760|gb|CF953891.1|CF953891
EST:     AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|58681274|gb|CK069961.1|CK069961
EST:     AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|218488951|gb|FG960688.1|FG960688
EST:     TTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: TTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|14571456|gb|BI118824.1|BI118824
EST:     AGGACAAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: AGGAC-AGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|58599567|gb|CK010095.1|CK010095
EST:     AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|29657069|gb|CB653344.1|CB653344
EST:     AGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATC-TTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
genomic: AGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|11544371|gb|BF475189.1|BF475189
EST:     AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCCTTGTGGTG
genomic: AAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTG
EST: gi|29626579|gb|CB631590.1|CB631590
EST:     TCAGGTTCTGTTTTATGAGCTTGATGCCA-TAGAAAAG                         GCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGT
genomic: TCAGGTTCTGTTTTATGAGCTTGATGCCATTAG-AAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGT

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: 51 (upstream exon), 75 (downstream exon)
Score: 35

GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaa ... taaaaactagGCATGTGCATCTTTGGAAGCCGATTATCAGCCACCCGTTACCTTTGTGGTGGTCCAGAAGCGTCATCACACAAGGCTGTTTGCTAATAACCACAAGGACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAGgtgattttaatttatctacttttcttctcaccatgaagttatctctctagtccccgactaacagttcaataaaaactag

- - - - - - - - - - - - - - - - - - - - -  GAGCTT