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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtagtatgctattgcacctgctcttagacatcaagttcctttcttaagtttgttacctgaattttagcaccttattttctcatgattcttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT

Basic information

species Oryza sativa
transcript LOC_Os10g42100.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 9
cttgtagtatgctattgcacctgctcttagacatcaagttcctttcttaagtttgttacc-tgaattttagcaccttattttctcatgatt-------cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT
   |  | | ||     |  ||||| |||| |||    ||  |||   || ||| |  || |  ||||  | | ||| |||| | ||| ||       ||||||| ||| ||| |  |||||||| ||||| | |||||| ||||| |||||||||||||| ||||| || |||||||| ||||||||| | || ||||| ||||| |
---ggcgaaggcaccatctgctgctattag-cat----tttgttttcgaaatttatatccatttatttcggtatcttgtttttttatgctttatgcttcttttggcagGGTCTACAGAACGAGGAGTTTTCCCCAAGCCAGCTAAGTAAAATGTTTGGATCCCATGCAACTATGATGGCCAACACCCTTCGGACACCAATCATTGTAT

upper sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G033526_T01 (Zea mays), 3'ss of exon 9
-----cttgtagtatgctattgcacctgctcttagacatcaagttcctttctta--agtttgttacctgaattttagcaccttattttctcatgattcttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT
            | |||| |||     ||  || |   ||||  |  | ||  |  | || | |  ||   ||||      |||| || | ||| ||||||||| ||| ||| |  || ||||| || || | |||||| ||||| |||||||| ||||||||||| || |||||||| ||||||||| |||| ||||| ||||| |
gcaaagacaccatctgctgttgt-ttagcattttgttttcaaaattatatccaattatttcgatgtcttgtttttg-----ttatgtt-ttatgcttcttttggcagGGTCTACAGAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTAT

upper sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 9
-cttgtagtatgctattgcacctgctcttagacatcaagttcctttcttaagtttgttacctgaattttagcaccttattttctcatgattcttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT---------
 | | |  | |  | | |||  |  | ||  | || |  | |  ||    | || | |  ||   ||||      |||| || | ||| ||||||||| ||| ||| |  || ||||| || || | |||||| ||||| |||||||| ||||||||||| || |||||||| ||||||||| |||| ||||| ||||| |         
ccatctgctgttgtttagcattttgttttcaaaattatatccaatt----atttcgatgtcttgtttttg-----ttatgtt-ttatgcttcttttggcagggtctacagAATGAGGACTTCTCCCCAAGCCAGCTAAGTAAAATGTTCGGATCTCATGCAACGATGATGGCCAACACCCTTCGCACACCAATCATTGTATTTACACAGA

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|58676860|gb|CK065547.1|CK065547
EST:     CAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|29661411|gb|CB657686.1|CB657686
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|29614922|gb|CB619935.1|CB619935
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|58669868|gb|CK058554.1|CK058554
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|58677681|gb|CK066368.1|CK066368
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|88333381|gb|CI642418.1|CI642418
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|66923995|gb|CX110843.1|CX110843
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|22307162|gb|BQ908384.1|BQ908384
EST:     ATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTTCGCAAAGCCAACTAAGCACAAATGTTTG
genomic: ATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAA-TTTTCGCAAAGCCAACTAAGCA-AAATGTTTG
EST: gi|218504586|gb|FG948260.1|FG948260
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|86519992|gb|CI160198.1|CI160198
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
EST: gi|29628928|gb|CB633939.1|CB633939
EST:     CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAG                         GCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA
genomic: CCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGA

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: 65 (upstream exon), 75 (downstream exon)
Score: 46

CCCACTGAAGGCAGTCAAGGTGATGCACACAGTGGCACAGAGAACAGAATCCAGCCTGTATAACCCAACTACATCTCCTAGTCTTGTTGCACATCCTCAGgtatatctct ... cttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaagtttgttacctgaattttagcaccttattttctcatgattcttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT
                                           ttctttt  CT-rich tract
               tgaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtagtatgctattgcacctgctcttagacatcaagttcctttcttaagtttgttacctgaattttagcaccttattttctcatgattcttttggtagGCTCTGCTCAACGAGGAATTTTCGCAAAGCCAACTAAGCAAAATGTTTGGATCTCATGCTACAATGATGGCGAACACCCTTTGCACCCCAATTATTGTGT

- - -agtatgc
- - - - - - tattgca
- - - - - - - - - -cctgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgaa