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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctggatcttgagagaggatgaacaaaagtcaatgtgaattcgaattcatataagcaaattctgctcaccttctgacgatgtatcgttctgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCATGAAGGATGGCCTCTCCGACAGCACCGTCCGGAAGAGCTTGGTCGGAGG

Basic information

species Oryza sativa
transcript LOC_Os03g52630.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52630.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G110735_T01 (Zea mays), 3'ss of exon 1
tcctggatcttgagagaggatgaacaaaagtcaatgtgaattcgaattcatataagcaaattctgctcaccttctgacgatgt-----atcgttctgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCATGAAGGATGGCCTCTCCGACAGCACCGTCCGGAAGAGCTTGGTCGGAGG
 | |  | ||  |   |   |||  || ||  |||| |    |  |  || | |      ||  ||   |   || |||||||      || |   ||| |||||| ||||||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||   |||||||||||||||
-cgtaaaactcaattaaaattgacgaagag--aatgagtgcaccga--cagaaactatgttttcgcctgctcactcacgatgttgtctgtcttctggaacgtcagCCGGTCCGCTGCCGAAGCACAACGGCGTCAGCTGGAGGGGCAATTCCTGCATGAAGGATGGCCTCTCCGACAGCACCGTCCGCCGGAGCTTGGTCGGAGG

upper sequence: LOC_Os03g52630.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 1
---tcctggatcttgagagaggatgaacaaaagtcaatgtgaattcgaattcatataagcaaattctgctcaccttctgacgatgtatcgttctgaa-tgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCATGAAGGATGGCCTCTCCGACAGCACCGTCCGGAAGAGCTTGGTCGGAGG
      |  |  ||||  |||   |||| |  |      || |  |  |   | ||   |   ||  ||   |   || |||| |  || |   ||| ||||||| || |||||||||||||| || ||||| ||||||||||| || || ||||||||||| |||||||||||||||||||||||   |||| ||||||||||
aagcgattaaaattgacggaga--gaacgagtgctgtgctgca--ccgacagaaattccccgttttcgcctgctcactcacgacgcgtcttctggaaatgtcagCCGGCCCGCTGCCGAAGCACAATGGCGTGAGCTGGAGGGGCAACTCCTGCATGAAGGACGGCCTCTCCGACAGCACCGTCCGCCGGAGCCTGGTCGGAGG
















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|58674076|gb|CK062762.1|CK062762
EST:     CCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: CCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
EST: gi|58664223|gb|CK052909.1|CK052909
EST:     GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
EST: gi|58669612|gb|CK058298.1|CK058298
EST:     GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
EST: gi|58609592|gb|CK037625.1|CK037625
EST:     GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
EST: gi|25797867|gb|CA753828.1|CA753828
EST:     GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
EST: gi|29634446|gb|CB639455.1|CB639455
EST:     CCCAGGACCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: CCCAGG-CCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
EST: gi|58665452|gb|CK054138.1|CK054138
EST:     CACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: CACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
EST: gi|29674435|gb|CB670710.1|CB670710
EST:     TTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: TTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
EST: gi|58662741|gb|CK051427.1|CK051427
EST:     GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGTGGGGAATTCTTGC
genomic: GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAG-GGGGAATTCTTGC
EST: gi|58669114|gb|CK057800.1|CK057800
EST:     GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGAT                         CTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA
genomic: GTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCA

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: 71 (upstream exon), 72 (downstream exon)
Score: 218

ATCGTCAAGCTCGTCCCCCACAAGCGCCCCCCTCCTCCTCCCCCCGACCAGTACACCCAGGCCCTCCACAAGGCCCTCATGTTCTTCAACGCGCAACGATgtgagttttt ... tgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCATGAAGGATGGCCTCTCCGACAGCACCGTCCGGAAGAGCTTGGTCGGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcatataagcaaattctgctcaccttctgacgatgtatcgttctgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCATGAAGGATGGCCTCTCCGACAGCACCGTCCGGAAGAGCTTGGTCGGAGG
                          ttctgac  putative branch site (score: 218)
                                       tcgttct  putative PPT
            aaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctggatcttgagagaggatgaacaaaagtcaatgtgaattcgaattcatataagcaaattctgctcaccttctgacgatgtatcgttctgaatgtcagCTGGTCCGCTGCCGAAGCATAACGGCGTCAGCTGGAGGGGGAATTCTTGCATGAAGGATGGCCTCTCCGACAGCACCGTCCGGAAGAGCTTGGTCGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- ctggatc
- - - - - - - - - - -gaacaaa
- - - - - - - - - - - - - - - -caatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -aagcaaa