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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTCCCTTGTCGCCTTACAGGACCTCACATTGGACAGGATCTTTGATGAGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactccttttcgcttaactcacacccttaagtgcatcatatttcagaaatcgctgagttgaaataaattaaaattatgttacattgcttaccatttttttccctgttttgtgtttag

Basic information

species Oryza sativa
transcript LOC_Os03g01890.1
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|87020805|gb|CI269522.1|CI269522
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|58690834|gb|CK079521.1|CK079521
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86827204|gb|CI270889.1|CI270889
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|87027547|gb|CI272312.1|CI272312
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|88842526|gb|CI081782.1|CI081782
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|87027592|gb|CI272357.1|CI272357
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCTGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86592956|gb|CI270513.1|CI270513
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86437466|gb|CI119188.1|CI119188
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|25803063|gb|CA759024.1|CA759024
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|88845000|gb|CI022354.1|CI022354
EST:     GTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: GTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|88901955|gb|CI374563.1|CI374563
EST:     TTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: TTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|88291958|gb|CI532550.1|CI532550
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86477934|gb|CI120567.1|CI120567
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCGAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|87038321|gb|CI192943.1|CI192943
EST:     GCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCA
genomic: GCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGC-AGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCA
EST: gi|58608625|gb|CK036658.1|CK036658
EST:     AGCCTGGAAAGGAGGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86524309|gb|CI164515.1|CI164515
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|88249928|gb|CI249777.1|CI249777
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|88253269|gb|CI351895.1|CI351895
EST:     AAAAGAAGCATTTTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTCCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|58591371|gb|CF989679.1|CF989679
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86478408|gb|CI121041.1|CI121041
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|87031788|gb|CI272489.1|CI272489
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86478930|gb|CI121563.1|CI121563
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86480411|gb|CI123044.1|CI123044
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|87040217|gb|CI194839.1|CI194839
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|163921032|gb|EG710408.1|EG710408
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|86481065|gb|CI123698.1|CI123698
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|89189338|gb|CI048877.1|CI048877
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
EST: gi|9788916|gb|BE530926.1|BE530926
EST:     AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAG                         GGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT
genomic: AGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCAT

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: 75 (upstream exon), 44 (downstream exon)
Score: 18

AACTTCCCTTGTCGCCTTACAGGACCTCACATTGGACAGGATCTTTGATGAGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactc ... ttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCATGTTTCTTTCGATCAGGCCGTGGCTTGGAAAGTGCTTGCCGAGGATAGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTTCCCTTGTCGCCTTACAGGACCTCACATTGGACAGGATCTTTGATGAGCCTGGAAAAGAAGCATTGTTCTCAAACATTCCCAAATTGATGGAGCAGgtagaaactccttttcgcttaactcacacccttaagtgcatcatatttcagaaatcgctgagttgaaataaattaaaattatgttacattgcttaccatttttttccctgttttgtgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG