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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaattttcacttcttagttcttaccttacatgctctcttaataagtaaaagttctgtatgatgtgtatgatccttatctatctctctgtgcttacttactgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG

Basic information

species Oryza sativa
transcript LOC_Os11g04980.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 12
gtttaattttcacttcttagttcttaccttacatgctctcttaataagtaaaagttctgtatgatgtgtatgatccttatctatctctctgtgcttacttactgtacc-agCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG
             ||||   ||||   || ||   |      |||   |||| ||||  |   |     |   |  |  | |     | | |  |    | |||| || |||||||||||||||||||||| |||||||||   ||||| |||||||| |||||| | || |||||||||||||||||||||||||||
-----------gtttctctcttctgctctgacccacgtagcaaattc-taaatgttcaatccaagcgaaactcttgtgctgtgatgatttatattggtcttctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTCACAGTGGACAATGGTCTCCTCACCCCAACATTCAAG

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 21
---gtttaattttcacttcttag-----------ttcttaccttacatgctctcttaataagtaaaagttctg----tatgatgtgta-tgatccttatctatctctctgtgcttacttactgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG
    | ||  |      || ||            || ||  || |       | |||| ||  | |  ||||      |  ||||| | |  |  |  ||||| | | | |   ||| |       ||| | |||||||||||||||||||||||||| ||  | ||   ||| || || ||  | || |||| ||| || || ||||||||||||
gtaatctatctcatctctcataagaaaagaaacatttttgtctgaacaaaaatgttaa-aaccagatcttctagtttcacaatgtgcagttcttttcttctatttattt-tatgtacatttcactgcagTTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAG
















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|33800033|gb|CF325882.1|CF325882
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|29671404|gb|CB667679.1|CB667679
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|58590451|gb|CF988759.1|CF988759
EST:     CAAGAGCTGCTGTCCTGNCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTAC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTAC
EST: gi|29618419|gb|CB623431.1|CB623431
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|29679208|gb|CB675483.1|CB675483
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|29679210|gb|CB675485.1|CB675485
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|29665943|gb|CB662218.1|CB662218
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|25806438|gb|CA762399.1|CA762399
EST:     AAGAG-TGGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: AAGAGCT-GCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|29665942|gb|CB662217.1|CB662217
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|29674249|gb|CB670524.1|CB670524
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|29670549|gb|CB666824.1|CB666824
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
EST: gi|29622335|gb|CB627346.1|CB627346
EST:     CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC
genomic: CAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTC

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: 50 (upstream exon), 61 (downstream exon)
Score: 10

TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaatttt ... actgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtatgatgtgtatgatccttatctatctctctgtgcttacttactgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG
                                        tacttac  putative branch site (score: 10)
                     ttatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaattttcacttcttagttcttaccttacatgctctcttaataagtaaaagttctgtatgatgtgtatgatccttatctatctctctgtgcttacttactgtaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC