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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatacatggtcttatactttctttgttcaaggattctagcatctgtttcctctctgactattgctaatgtataaatgtgataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT

Basic information

species Oryza sativa
transcript LOC_Os12g03480.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03480.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
--gttagtatacatggtcttatactttctt-tgttcaaggattctagcatctgtttcctctctgactattg-ctaa---tgtataaatgtg-ataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT
  || |       |  | | | |  || |  || |     | ||  | |    | | |    |||   |   ||||   ||| | ||| |   |    || |||||||| ||||| ||||| ||||||||||  || |  |||||||||||||| |||||| ||||   || ||||   || ||||| || || |   ||
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT

upper sequence: LOC_Os12g03480.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
gttagtatacat---ggtcttatactttctttgtt--caaggattctagcatctgtttcctctctgacta--ttgctaatgtataaatgtg-ataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT
  ||  ||   |     ||| ||  |    | |||   ||    | ||| ||   |   |    || |||   |  || ||| | ||| |   | |  || |||||||||||||| ||||| ||||||||||  || |  |||||||||||||| |||||| ||||   || ||||   || || || || || |   ||
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT

upper sequence: LOC_Os12g03480.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S106_48V6.2 (Physcomitrella patens), 3'ss of exon 17
-----gttagtatacatggtcttatactttctttgttcaaggattctagcatctgtttcctctctgact--attgctaatgtataaatgtgataac--cagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT
        || |||       || | ||  ||    | ||| |   ||  || | |   |   |||| |  |  |   || |||   |||| |  |  ||| |||||||||||||| ||||| |||||||| |||||||| || || || || || || ||| | |||   |  ||     | || | ||||||     ||
catcacacagaatagtccactttttcctccctaaaataaagaacagtaa-atttctacgcatactgagtggaagggacatttatgtgtgtgttcgcaacagATGGAACCCAGATGCAATTGTTTTCAACTCTTGGCAACAATACGGGACACCCAGCTACTGGGTTCAGCATTTCTTTAAAAACTCCAACGGTGCCGACCTT

upper sequence: LOC_Os12g03480.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
----gttagtatacatggtcttatactttctt---tgttcaaggattctagc--atctgtttcctctctgactattgctaatgtataaatgtgataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT
    |   ||  |  |  || ||| | |  |         | | |||  |    |   |  |     ||||  |   |||     |   |||| | ||||| |||||||| ||||| ||||||||||||||||||||||||||||| || || || || ||| | ||   || ||||    |||| | ||| ||     | 
tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaaa-actagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC

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|25803487|gb|CA759456.1|CA759456
EST:     GTTCAGATGGCATGTTATGCACCACTTTTCGTGAATGACAACGATCGCGT                         CTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCC
genomic: GTTCAGATGGCATGTTATGCACCACTCTTCGTGAATGACAACGATCGCGTgttagtatac ... tgataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctagcatctgtttcctctctgactattgctaatgtataaatgtgataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT
                             tgctaat  putative branch site (score: 2)
                                taatgtataaatgt  TA-rich tract