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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatgttttgttctgaataaaccgaaagcatttgatattttcttgaattcctagctatttctcactcaatacgattatctgatgtttccaaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G359566_T01 (Zea mays), 3'ss of exon 1
-------agaatgttttgttctgaataaaccgaaagcatttgatattttcttgaattcctagctatttctcactcaatacgattatctgatgtttccaaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC
       | |    ||  ||||||  |||  | |||    ||| |||| |||    | | | ||||| |||||| |     ||||| || |    |||| | | ||| | |||||||||||||||||||| |||||||| ||||||||||||   || |||| | |||||||||||||||||| ||| ||||| |||||||    ||
ttcctcgaaagcacttgattctgataaaattggaagttactgacattt-cttatcctgcca-ctattactcacttac----attatttg-tacccccaatcgtacagACCGGTGTTGCTGTCAAACATTGTAAGGAGGGCACTGAGAGCTCTATTTTCTGGTCTTCTCTTGGTGGAAAGCAGAGTTATACAAGTAGAAATGTTGTAC

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 16
------agaatgttttgttctgaataaaccgaaagcatttgatattttcttgaattcctagctatttctcactcaatacgattatctgatgtttccaaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC
        |    ||  ||||||  |||  | ||  | |||| |||| |||    |     ||||| | |||| ||    |||||||| |    |||| | | ||| | |||||||||||||| |||||||||||||| ||||||||||||   || |||| | || ||||||||||||||| ||| ||||  ||||||||  |||
tcctcggcagcacttgattctgataaaataggaactaattgacattt-cttatcgtgtcgactattacccacttaa----attatctg-tacccccaatcctacagACCGGTGTTGCTGTCAAGCATTGCAAGGAGGGCACTGAGAGCTCTATTTTCTGGTCTTCTATTGGTGGAAAGCAGAGTTATACAAATAGAAATGCTGCAC

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 15
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 15
--------------agaatgttttgttctgaataaaccgaaagcatttgatattttcttgaattcctagctatttctcactcaatacg-attatctgatgtttccaaacttg-cagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC
                | ||| ||||| | | |  | |  ||   |||   |      |   | | |  |  |||  |||  ||  |  | ||    |||| |      |   ||||| ||  || || |||| |||  ||| || ||||| ||||||||  ||||||||||||| ||||| ||||| ||||||| ||| ||||  || ||  |  
gttagtttctggttgtactgtgttgttttcagtttatcttaaatctttccaa-----ataggtgctttacagttttacacggaactcataatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 15
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 16
------------------------------------------------------agaatgttttg-ttctgaataaaccgaaagcatttgatattttcttgaattcctagctatttctcactcaatacgattatctgatgtttccaaacttgc------agCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC
                                                       ||||| | |  || | | ||| |    |  | |  | | |  || | | | ||    | || ||  | | |   |   |      | | |   |||||      |||||||   | || |||| ||    || |||||||| ||||||||  ||||||||||||| ||||| ||||| ||||| | ||| ||||  || |   |  
gtagtttctaatggtgttatctttgattttaatttagctgaaattgtccaagtaggaatggtataatttttattaagctttta--aataaaaactcactcgtacttcttatcacttttctgtaactggtaaacttaatcatcttctttcttgctaagtcagCCTGGGACTACTATCAAGCACGCAAAAGAGGGAACAGAGAGCTCATCCTTTTGGTTTGCACTTGGGGGAAAACAGAACTTCACCAGCAAGAAAGTTTCCT

upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 14
-agaatgttttgttctgaataaaccgaaagcat-ttgatattttcttgaattcctagctatttc---tcactcaatacgattatctgatgtttccaaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC
 | ||  |    ||  | ||    |   |  |  ||| |      |  |  |  ||  ||||     | | | | |  |||   ||  |||||  ||   | ||||| || ||  || | ||||||   || || |||||||||||||| |||||||||||||| ||||| ||||| |||||||||||||||| ||| ||  | |
gataacatgcccttgggcatctttctgtaatagattgtttgacgatcaagattgtatatattgtggtttattaattgagatccact--tgtttataa---ttcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC

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|58670584|gb|CK059270.1|CK059270
EST:     GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
EST: gi|88351837|gb|CI624642.1|CI624642
EST:     GTTCGTATGAACAGCAACAATGGGCTGGAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
EST: gi|25798468|gb|CA754429.1|CA754429
EST:     GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
EST: gi|88722817|gb|CI746327.1|CI746327
EST:     GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
EST: gi|12404685|gb|AU166286.1|AU166286
EST:     GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
EST: gi|426363|gb|D22226.1|D22226
EST:     GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGNCAAACATTGCAAGGAGGG
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGG
EST: gi|58674368|gb|CK063054.1|CK063054
EST:     GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
EST: gi|58610643|gb|CK038355.1|CK038355
EST:     TGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCGAGGAGGGAACTGAGAGCTCTGGCTTT
genomic: TGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
EST: gi|58672994|gb|CK061680.1|CK061680
EST:     GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
EST: gi|88569524|gb|CI660699.1|CI660699
EST:     GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAG                         CCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT
genomic: GTTCGTATGAACAGCAACAATGGGCTGCAAAAGTTGCTGAATTCTTGAAGgtatgaaatg ... aaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattcctagctatttctcactcaatacgattatctgatgtttccaaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC
           tatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatgttttgttctgaataaaccgaaagcatttgatattttcttgaattcctagctatttctcactcaatacgattatctgatgtttccaaacttgcagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA