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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttccgctcttcttcctccattttttctttaatttttttttgtttatatcgttgccctcttgagaaatggtgcttaatccgttccatggattggtttgggttcgtgcgctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC

Basic information

species Oryza sativa
transcript LOC_Os03g52840.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------gttccgctcttcttcctccattttt--tctttaatttttttttgtttatatcgttgccctcttgagaaa---tggtgcttaatccgttccatggattggtttgggttcgt--------gcgctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
                                                     || || |||  |    | |||    | ||   |         |  |  |    |      |||||    |   | | ||||||||    |||| | || | || ||        | |  | ||||||||||||| |||||||||||||||||||||||| |||||
gtacgacaccgactgctgcttcttgttcttattatcgtggcacggcgccacggcggtcatctgtcattgtctttgtcttctaccctacccacccctcgaaagaaaacaaacaaagaaagcacgactcatgatccgttcttctgatttgatttgatttgtttttttttgtgtgcgcgcagGCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC
















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|58592438|gb|CF990746.1|CF990746
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88424270|gb|CI581825.1|CI581825
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88428580|gb|CI565048.1|CI565048
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88760569|gb|CI770125.1|CI770125
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|29634685|gb|CB639694.1|CB639694
EST:     ACACCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGACATATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88734102|gb|CI757610.1|CI757610
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88397959|gb|CI583277.1|CI583277
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGAGGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88424301|gb|CI581856.1|CI581856
EST:     ACGCCCTCCGCCGCCAGCCGTTCTCCCGCATCACCCCGCTCTATTACATG                         GCGTCCCTGCCGGGGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88398541|gb|CI595942.1|CI595942
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCAACCCGCTCTACTACATG                         GCGT-CCTGCCGGCGACGGAGGAGAGATTCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88826721|gb|CI777286.1|CI777286
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88344989|gb|CI625835.1|CI625835
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCATCCCGTTCTACTACATG                         GCGTCCCTGCCGGCGATGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|58605751|gb|CK033784.1|CK033784
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88745591|gb|CI768951.1|CI768951
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGAAGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|87023586|gb|CI286337.1|CI286337
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|88733450|gb|CI756627.1|CI756627
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|86901078|gb|CI306267.1|CI306267
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|58691682|gb|CK080369.1|CK080369
EST:     ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
EST: gi|58605862|gb|CK033895.1|CK033895
EST:     AAGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATG                         GCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
genomic: ACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC

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), 39 (downstream exon)
Score: 56

CCGCTCGCCCACCATGGCCATGGCGACGGCGCTCCGCAAGCTCTCCTCCGACGCCCTCCGCCGCCAGCCGCTCTCCCGCATCACCCCGCTCTACTACATGgttccgctct ... gctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatggtgcttaatccgttccatggattggtttgggttcgtgcgctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC
         gcttaat  putative branch site (score: 56)
                                            cgctctc  putative PPT
           ttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccgctcttcttcctccattttttctttaatttttttttgtttatatcgttgccctcttgagaaatggtgcttaatccgttccatggattggtttgggttcgtgcgctctcgcagGCGTCCCTGCCGGCGACGGAGGAGAGATCCGGAGTCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC