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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagcaaactattgtaattttagttatttctgggatatatatgaatctgttttcctgctattttccctccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTACATCATCAAAATCCTTCCGTGGTCCTGGTCTGGAGGAAGGCCTGAAG

Basic information

species Oryza sativa
transcript LOC_Os12g10784.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g10784.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 3
-----------gtgagcagcaaactattgtaattttagttatttctgggatatatatgaatctgttttcctgctattttccctccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTACATCATCAAAATCCTTCCGTGGTCCTGGTCTGGAGGAAGGCCTGAAG
           ||| | | ||  || || |  || ||   |   | ||| || || | || ||    |  |||  ||  | |||||  ||||||||||  | || || ||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||| || ||||| || |||
gtgagcacgaagtggggatcagtct-ttttttttctaacaaaaccggggctaaat-taaacctacactgttgcctttccctctccatgatagGCTTGGAATTCCGCTCGTGTTCAAGTCCAGCTTTGATAAAGCAAACCGTACATCATCAAAATCATTCCGTGGTCCTGGTCTTGAAGAAGGTCTTAAG

upper sequence: LOC_Os12g10784.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 2
-------------------gtgagcagcaaactattgtaattttagt--tatttctgggatatatatgaatctgttttcctgctattttccctccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTACATCATCAAAATCCTTCCGTGGTCCTGGTCTGGAGGAAGGCCTGAAG-
                   ||||     |   | |||||    |  |  || || |    |  |    ||  || | |   |    | |   ||    | ||  ||||  | ||| | || |||||||| |||||||| ||||| || || |||||||||||||| || ||||| || ||  |||  || ||  ||||| 
aagggtcaaagttaaaattgtgaatgaaatggt-ttgtagacatgatattagttttatctttgaagctaacatgatcttgagtgtatatgtgtctttcagaG--TTGGAATACCATTGGTTTTCAAGTCAAGCTTTGACAAAGCTAACCGAACATCATCAAAATCATTTCGTGGCCCGGGGATGGCTGAGGGATTGAAGG

upper sequence: LOC_Os12g10784.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------gtgagcagcaaactattgtaa-----ttttagttatttctgggatatatatga-atctg---ttttcctgctattttccctccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTACATCATCAAAATCCTTCCGTGGTCCTGGTCTGGAGGAAGGCCTGAAG
                                                          |     | || | |||  ||     |   ||  |   | ||  ||||| ||| | ||    |  || ||    | |   |       ||  ||||  | ||  | || |||||||| |||||||| ||||| || || |||||||||||||| || ||||| || ||  |||  || ||  |||||
gtatgtaattatctctatttatgattattttttttattaatgggaaaataaatgtgatttgatggaaatccattagaaaaagctagcaggaagaacgggtgtatatttgatagctaacatgatcttgagtgtatatgtgtcttccagAGTTGGAATACCGTTGGTTTTCAAGTCAAGCTTTGACAAAGCTAACCGAACATCATCAAAATCATTTCGTGGCCCGGGGATGGTTGAGGGATTGAAG

upper sequence: LOC_Os12g10784.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 2
gtgagcagcaaactattgtaattttagttatttctgggatatatatgaatctgttttcctgctattttccctccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTACATCATCAAAATCCTTCCGTGGTCCTGGTCTGGAGGAAGGCCTGAAG
||  |         || | || |||  || ||| |  | | | |  | || ||||     | | | ||          |||  ||||  ||   || || |||||||| |||||||||||||| ||||| || || |||||||| || || ||||||||  ||   ||||||||||||
gtatgttttgtttgatggaaaatttcattgtttttacggtttgt--ggat-tgttcatagggtttgttttacaatttctagATTTGGGTTGAAGCTGGTTTTCAAGTCGAGCTTTGATAAAGCCAATCGAACCTCCTCAAAATCATTTCGGGGTCCTGGCATGATTGAAGGCCTGAAG

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|58681266|gb|CK069953.1|CK069953
EST:     GAGGAGCATGTCCTGAAGATGGCAAAACACATCGAAGGCATCACAACCAA                         GCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
genomic: GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAAgtgagcagca ... tccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
EST: gi|33681873|gb|CF310112.1|CF310112
EST:     GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAA                         GCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
genomic: GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAAgtgagcagca ... tccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
EST: gi|88433551|gb|CI594365.1|CI594365
EST:     GAGGAGCATGTCCTGAAGATGGCAAAACGCATCAAAGGCATCACAACCAA                         GCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
genomic: GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAAgtgagcagca ... tccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
EST: gi|58589242|gb|CF987550.1|CF987550
EST:     GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAA                         GCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
genomic: GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAAgtgagcagca ... tccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
EST: gi|41883464|gb|BX928437.1|BX928437
EST:     GAGGAGCATGTCCTGAAGATGGCCAAACACATCAAAGGCATCACAACCAA                         GCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
genomic: GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAAgtgagcagca ... tccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
EST: gi|88332901|gb|CI639749.1|CI639749
EST:     GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAA                         GCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC
genomic: GAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAAgtgagcagca ... tccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatttctgggatatatatgaatctgttttcctgctattttccctccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTACATCATCAAAATCCTTCCGTGGTCCTGGTCTGGAGGAAGGCCTGAAG
                       tctgttttcctgctat  CT-rich tract
            atatatatgaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcagcaaactattgtaattttagttatttctgggatatatatgaatctgttttcctgctattttccctccacaatagGCTTGGTCTGCCACTTGTGTTCAAGTCCAGCTTTGATAAAGCAAATCGTACATCATCAAAATCCTTCCGTGGTCCTGGTCTGGAGGAAGGCCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG