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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTACCTGTTGTCACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgttaacacaatatattttgatttcttagtgcatgaaaatctttaacgcatgcctcttactctgcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g42260.3
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G022383_T02 (Zea mays), 5'ss of exon 10
TGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTACCTGTTGTCACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgttaacacaatatattttgatttcttagtgcatgaaaatctttaacgcatgcctct-tactctgcgcag
| |||| ||||| || ||||||||||||||| ||||||||  |||||| ||||||||  ||||||| || ||||| ||||||||||| ||||||||||||||    |   || |||| ||  | |   ||    |||    || ||   ||||   |  |  || | || ||  |||
TTCTGAGGTTGCCAAAGCACGTGCAAGTGCAGCCAAAGTTGTCTGTTGCCACTTCTCAGCTGATGGTAAGCTGCTTGCTACTGGTGGTCATGATAAAAAGgtatgatcactaccaca-taactatcatttcagaagttttagagaaagcttaaattacccacctgttctttgtacag

upper sequence: LOC_Os01g42260.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G425377_T01 (Zea mays), 5'ss of exon 5
TGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTACCTGTTGTCACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgttaaca-----caatatattt-tgatttcttagtgcat-gaaaatctttaacgcatgcctct-tactctgcgcag
| |||| ||||| || ||||| |||||  || ||||||||  |||||| ||||||||  ||||||| |||||||| ||||||||||| |||||||||||||||   |   || ||     | | |||  | | |||||  | |   | || |    ||||   |  |  || | || ||  |||
TTCTGAGGTTGCCAAAGCACGCGCAAGCACAGCCAAAGTTGTCTGTTGCCACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcactaccagtctaccacataactatcatttcacaatttttagagagagcttaaattactcacctgttctttgtacag

upper sequence: LOC_Os01g42260.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA05G08110.1 (Glycine max), 5'ss of exon 13
TGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTACCTGTTGTCACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgttaacacaatatattttgatttcttagtgcatgaaaatctttaacgcatgcctcttactctgcgcag---------------------------
     |  |   | |   |   |||||| |    ||||||   |||||||||||||| || ||||| ||||| || ||||| ||||| |||||||| |||||     || ||     ||  |  || |  | | |    |     || || |    |    |   | |  | | |                            
CAAGAATATGAAGCATATAATGGCAAGTTCGCATAAAGTTGAGTGTTGTCACTTCTCATCAGATGGAAAACTTCTTGCTACAGGTGGCCATGATAACAAGgtatg--tgctagattgatccaactttagctatgaaatgacctccat-ttcagtagaaatgttgcatttagtggatgttggaagaaactttggtttcttgatt

upper sequence: LOC_Os01g42260.3 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv11s0016g04550.t01 (Vitis vinifera), 5'ss of exon 13
TGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTACCTGTTGTCACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgttaacac--aatatattttgatttcttagtgcatgaaaatctttaacgcatgcctcttactctgcgcag------------------------------------------------------------------
| | |||||   |        ||||||| |||  ||||||   |||||||||||||| || ||||| |||||||| || |||||||| || ||||||||||||  | ||   | ||  || |  |||||   | ||  | || || |      | |   |||| |||    ||   |                                                                   
TTCGGAAGTCCGGTGTATTACTGCAAGTACAAGTAAAGTTGAATGTTGTCACTTCTCTTCAGATGGAAAACTGCTTGCCACTGGTGGGCAGGATAAAAAGgtgaggatggatataccaaaaaagttttgtgatattgattcaggaga----caagcttttgccacttgaattgaataacattgtttttgggacatttcatgaaagataacatcaatctctttgcttcttgattttataatgcag

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|33794564|gb|CF323169.1|CF323169
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|58665681|gb|CK054367.1|CK054367
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|58608277|gb|CK036310.1|CK036310
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         G-TCTGGTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|33794705|gb|CF323235.1|CF323235
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|66923385|gb|CX110233.1|CX110233
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|58604540|gb|CK015068.1|CK015068
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|32948512|gb|BP185084.1|BP185084
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|58598175|gb|CK008703.1|CK008703
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|218488081|gb|FG946110.1|FG946110
EST:     CGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: CGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|3107649|gb|D43389.1|D43389
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTACCTGTTGTCACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgttaacacaatatattttgatttcttagtgcatgaaaatctttaacgcatgcctcttactctgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA