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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtcgcgtcctcctcctcctccggtgaccgtccgggctagggtttcccgccgccggcgtgaggctcatgcgtgcgtgtgcgtgtgcgtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGAGGCAAGTCCA

Basic information

species Oryza sativa
transcript LOC_Os02g13530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G091383_T01 (Zea mays), 3'ss of exon 1
gtgcgtc-gcgtcctcctcctcctccggtgaccgtccgggctagggtttcccgccgccggcgtgaggctcatgcgtgcgtgtgcgtgtgcgtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGAGGCAAGTCCA
    ||| | |   | | |   |  |||   || ||   || ||    || ||        | ||   | | ||||| |   || ||    | | |||||||||| || ||||||| |||||| ||| ||||||||||||||||  |||||||||||||||| |||||||||||||||||||||||||| |||||||| |
----gtcagtgcggtgcccaagcgtcgg-agccttcgctgcgagatcctctcgttctattagcgattttgacgcgtgtgatcgcttg---atat-tgcagGCGGAGCTCAAGGAGAGGCTGGCTAAGATGTACGAGGTGAAGGATCCCAACTGCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCTA

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S450_9V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------gtgcgtcgcgtcctcctcctcctccggtgaccgtccgggctagggtttcccgccgccggcgtgaggctcatgcgtgcgtgtgcgtgtgcgtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGAGGCAAGTCCA
                              ||| |  | ||  |    |   |  ||     |||   | ||||||||   |  |  ||   |  ||| | |        | ||   |  |     ||||| || |||||||||||||| ||||||||||||||||||  |||  || |    ||||||||||||  |||| | ||||| || ||||| ||||||||||
gtgagtggcccactggaagctctatgtgttgtgtggtgtgtaatggcacatttttgggtttagtcgaagttagggtttt--gttggagg-acggagctgagg--------ttcgatggttttcactcagGCTGAGCTGAAGGAGAAGCTCGCGAAGCTGTACGAGGTGCGGGATCCCCAGACTATCTTCGTGTTCGGGTTCAGGACCCAGTTTGGAGGTGGCAAGTCCA

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------gtgcgtcgcgtcctcctcctcctccggtgaccgtccgggc--tagggtttcccgccgccggcgtgaggctcatgcgtgcgtgtgcgtgtgcgtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGAGGCAAGTCCA
                      || |   | ||  | |      || |  ||      | ||  | | |||||  |  |||      |     |   | | ||  | ||||  |      ||||| || |||||||| |||||||| |||||||||||||| |  ||  || |   |||||| ||||||  |||| | || || |||||||| ||||||||||
gtgtgtgtttcattgcaacctggttcactgtgtgttgcgttgtttcggtagagttgttgtgcggtcgagtttcgggttgccccaaaaaaagagagctgagagt-cgtgtgt-tgatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAGACCATCTTTGTGTTCGGGTTCAGAACGCATTTCGGAGGTGGCAAGTCCA

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|89165150|gb|CI255207.1|CI255207
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|87031413|gb|CI261787.1|CI261787
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|87007097|gb|CI277172.1|CI277172
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|86416175|gb|CI030186.1|CI030186
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|3762404|gb|C99652.1|C99652
EST:     GGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCNAC
genomic: GGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|86510587|gb|CI153220.1|CI153220
EST:     CGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: CGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88208253|gb|CI208102.1|CI208102
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88524829|gb|CI453780.1|CI453780
EST:     CCAACGTCTCCAGG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: CCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|38471297|gb|CF955428.1|CF955428
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|86420572|gb|CI056561.1|CI056561
EST:     AGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88242685|gb|CI242534.1|CI242534
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|8336460|gb|BE040907.1|BE040907
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88241783|gb|CI241632.1|CI241632
EST:     GGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: GGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|87022540|gb|CI267677.1|CI267677
EST:     CTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: CTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC

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: 74 (upstream exon), 75 (downstream exon)
Score: 175

GGTGACGCTCCGCACCCGCAAGTTCATGACGAACCGCCTCCTCTCCCGCAAGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtcgcg ... gtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGAGGCAAGTCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtcgcgtcctcctcctcctccggtgaccgtccgggctagggtttcccgccgccggcgtgaggctcatgcgtgcgtgtgcgtgtgcgtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGAGGCAAGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG