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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcgccaacggccaagctatttcaaacatgagttaatatagtattatcgagtagtaactaaacgtgatcaaattttcattctttttttggttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTATGCCTGCTGCCACTGTTCCACATCTACTCGCTCAACTCCGTGCTGCTGG

Basic information

species Oryza sativa
transcript LOC_Os02g08100.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08100.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G075333_T01 (Zea mays), 3'ss of exon 1
--tggcgccaacggccaagctatttcaaacatgagttaatatagtattatcgagtagtaactaaacgtgatcaaattttcattctttttttggttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTATGCCTGCTGCCACTGTTCCACATCTACTCGCTCAACTCCGTGCTGCTGG
   |        | | |  | ||  |   | |  |       | | |       ||    || ||  || |   | | ||   ||  |  ||  | |||||||| ||||| |||||||| |||||||||||| ||||||| || ||  | || ||||||||||| |||||||||||||||||||| ||||| ||||||||||
ttcgagattcgtgccgagacgatgcctgtccttcgcattcgaactgtgtgttgatacatgctgaaactg-tgggagtgtctggctgctgatgaat-atgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTGTGCCTGCTGCCGCTGTTCCACATCTACTCGCTGAACTCGGTGCTGCTGG
















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|88301992|gb|CI667838.1|CI667838
EST:     AGGGCGTCATGCTCACCCACCGNAGCCTCATCACCAGCGTCGCCCAGCAG                         GTGGATGGAGAGAACCCTAACCCGTANTTCAGCAAGGATGATGTTATACTA
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
EST: gi|88326599|gb|CI658315.1|CI658315
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAG                         GTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
EST: gi|29657755|gb|CB654030.1|CB654030
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAG                         GTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
EST: gi|29659213|gb|CB655488.1|CB655488
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAG                         GTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
EST: gi|58677400|gb|CK066087.1|CK066087
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAG                         GTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
EST: gi|29657567|gb|CB653842.1|CB653842
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAG                         GTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
EST: gi|29688318|gb|CB684593.1|CB684593
EST:     AGGGCGCCTTGCTAACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAG                         GTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
EST: gi|58606049|gb|CK034082.1|CK034082
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAG                         GTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTA

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), 69 (downstream exon)
Score: 53

CGACGACGTCGTCGCCCTCCCCTACTCCTCCGGCACCACCGGCCTCCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctc ... gttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTATGCCTGCTGCCACTGTTCCACATCTACTCGCTCAACTCCGTGCTGCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcgagtagtaactaaacgtgatcaaattttcattctttttttggttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTATGCCTGCTGCCACTGTTCCACATCTACTCGCTCAACTCCGTGCTGCTGG
                            ttttcattcttttttt  CT-rich tract
                      atcaaattttcattct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcgccaacggccaagctatttcaaacatgagttaatatagtattatcgagtagtaactaaacgtgatcaaattttcattctttttttggttcatgaagGTGGATGGAGAGAACCCTAACCTGTACTTCAGCAAGGATGATGTTATACTATGCCTGCTGCCACTGTTCCACATCTACTCGCTCAACTCCGTGCTGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - -gccaagc
- - - - - - - - - - - tcaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatcaaa