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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcctttctatgatctatgatttgttcttcttttatattttgcaaggatgaacctggttaactaggctcccacattcttttgctacttttctatttctactgagacgtctgagaacgcttgagtagatttagctcattttgttttatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAGATGTGGCCTATCTGTATGGAGAAGATCGTCTCACAACTTCTACGACCCA

Basic information

species Oryza sativa
transcript LOC_Os01g14050.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G144403_T01 (Zea mays), 3'ss of exon 3
gtatgctcctttctatgatctatgatttgttcttcttttatattttgcaaggatgaacctggttaactaggctcccacattc-ttttgctacttttctatttctactgag--acgtctgagaacgcttgagtagatttagctcattttgttttatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAGATGTGGCCTATCTGTATGGAGAAGATCGTCTCACAACTTCTACGACCCA
|||||| ||||      || |    ||  | |   ||||| || ||||| |||| |   | ||| ||||||||   |  ||| || | || ||||||  || || ||     | | |||     || || ||| ||  ||||||| |||||||||||||||||| || |||||||||||||||| ||||||||||||  |||||||  | |||||||||||| ||||||||||||||||||| ||| |||||||||| ||||
gtatgcacctt-----aattttctgttgctgcactttttaaatattgcatggataagtattgttgactaggctggaaatttcattctactccttttcatttccttcttttttatgactgttcctgcctgtgtacatccagctcatattgttttatgtatcagCTCCTCTCTGATGCAGAATCAGCACGCTGGTTAAACCATGCAATCGACAAGATGTGGCCTGTCTGTATGGAGAAGATCGTTTCAAAACTTCTACGGCCCA
















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|88368176|gb|CI575058.1|CI575058
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
EST: gi|88431214|gb|CI574385.1|CI574385
EST:     GCGGAAGAGAATACAACCATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGGCTATCTGATGCAGAATCAGTAGGCTGGTTAAATTATGCAATAAAAAA
genomic: GCGGAAGAGAATACAAC-ATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTG-CTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAA
EST: gi|58690106|gb|CK078793.1|CK078793
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
EST: gi|88694531|gb|CI738569.1|CI738569
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAATCAGTACGCTGG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGG
EST: gi|88763700|gb|CI773119.1|CI773119
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAATCAGTACGCTGGTT
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTT
EST: gi|88389854|gb|CI626623.1|CI626623
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
EST: gi|88449626|gb|CI579906.1|CI579906
EST:     TGCGGAAGAGAATACAAAATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAATCAGTACGCTGG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGG
EST: gi|88743560|gb|CI767068.1|CI767068
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAA
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAA
EST: gi|88410896|gb|CI578702.1|CI578702
EST:     TGGGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACGAAGGAAGA                         GTGCTATCTGA
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGA
EST: gi|117233805|gb|CT847747.1|CT847747
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
EST: gi|88358378|gb|CI606887.1|CI606887
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGGCTACCAAGGAAGA                         CTGGTATCTGATGCAG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAG
EST: gi|88397069|gb|CI593281.1|CI593281
EST:     TGGGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTAGCAACGAAGA                         CTGGTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
EST: gi|88368269|gb|CI575151.1|CI575151
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
EST: gi|88445398|gb|CI584511.1|CI584511
EST:     TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGA                         CTGGTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG
genomic: TGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAG

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), 66 (downstream exon)
Score: 12

GTAAATGCTCGCTGTGCAATGAAATTGCGGAAGAGAATACAACATGAAGAAATGAAATCTGCCTACCAACGAAGAgtatgctcct ... tatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAGATGTGGCCTATCTGTATGGAGAAGATCGTCTCACAACTTCTACGACCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagacgtctgagaacgcttgagtagatttagctcattttgttttatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAGATGTGGCCTATCTGTATGGAGAAGATCGTCTCACAACTTCTACGACCCA
                                     ttttgtttt  CT-rich tract
                                    attttgttttatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcctttctatgatctatgatttgttcttcttttatattttgcaaggatgaacctggttaactaggctcccacattcttttgctacttttctatttctactgagacgtctgagaacgcttgagtagatttagctcattttgttttatgtatcagCTGCTATCTGATGCAGAATCAGTACGCTGGTTAAATTATGCAATAAAAAAGATGTGGCCTATCTGTATGGAGAAGATCGTCTCACAACTTCTACGACCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA