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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCACGAAAACCCTCTGCCTCCTTCGCTCGCTGCACCCTCGTCTCGGCGATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattccccccagcactagtcgtctcacaatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g62420.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G146206_T02 (Zea mays), 5'ss of exon 1
--CTCCACGAAAACCCTCTGCCTCCTTCGCTCGCTGCACCCTCGTCTCGGCGATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattccccccagcactagtcgtctcacaatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcag
  ||||||     ||  ||  |     ||   ||| | ||    ||  |  |  | | | |||||| |||||||||||||||| || |||||||||||||||||||||   ||||| || ||     |   ||    |||   | |    ||   | |  ||  | |    || | |  || |||   | |   ||||   | ||||    | | ||||||
AACTCCACTGTCTCCAACTCTCCATCGCGTCTGCTACGCCTC--TCCTGCAGGACGACCAATGGCTTCCAGGAAGTTCTTCGTGGGTGGCAACTGGAAATGCgtaagt---ccccctaggacccag-gctccaggcaccaccgttctctcgatttgaattcgacgttacgcagagttttggtttgatctct---gatggcatccgctccc-ccgtgtgcag

upper sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA13G41120.1 (Glycine max), 5'ss of exon 1
---CTCCACGAAAACCCTCTGCCTCCTTCGCTCGCTGCACCCTCGTCTCGGCGATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattccccccagcactagtcgtctcacaatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcag
      |         ||||| || ||||  || ||   | ||||| ||        |   ||    | ||| || ||||||||||| |||||||||||||||||| || |    | |     |   | | |  |  |     ||   |     ||||      |  | ||    ||||||   ||   | |   |  |  || | ||              
GTTTCTCTTTCTCTTTCTCTGTCTGCTTC-TTCACT-TTCTCTCGTTTCAATCGAA-AAAAATCATGGGCAGAAAATTCTTCGTCGGTGGCAACTGGAAATGCgtatgtttcaatcactatcttcaccatttacctttttttttttttgcatgtccggtttttgttttaatct-cgatgag---tgaaatct-cggtagttctactct--------------

upper sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G55440.1 (Arabidopsis thaliana), 5'ss of exon 1
CTCCACGAAAACCCTCTGCCTCCTTCGCTCGCTGCACCCTCGTCTCGGCGATCCATCC-ATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattccc--cccagcactagtcgtctcacaatccagattccggatgagccggagacgctgctgat-gagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcag
   | | |    | || |  ||  |  ||| |   | | ||| ||     |    |   ||    ||||| |||||||||||||| |||||||||||||| ||||||  ||    ||    | |   |  || |  ||    | ||  |     |  ||  |    | |||  ||| |    | | ||    |  ||||     |                  
TCTCTCCATCGTCGTC-GTATCTGTGACTCTCGTGATCATCGCCTGAAAAAAATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatctttaccttctattgcgcaccttattatt---agtcttgtc--acttgatccttccccgatcaagtcaaagagatcggaaaatcccgatcttaaga-----------------

upper sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv13s0019g01090.t01 (Vitis vinifera), 5'ss of exon 1
CTCCACGAAAACCCTCTGCCTCCTTCGCTCGCTGCACC-CTCGTCTCGGCGATC--CATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattccccccagcactagtcgtctcacaatccagattccggatgagccggagacgctgctgatgagtgatgag-gcttgggt--tttatcgatgcgctgcgctgttgctgcgtgcag
    | | |     |  | ||  ||     ||| |     | | ||  | |||   | ||   |   | ||| || |||||||||||||||||||||||||||||| || | |   |   | ||   | | ||   ||    |||     |   |         |  |  |   |  |    | |||| |  |||  |||| |                      
---GAAGCAGCTGTTAAGACTTTTTTTTCTGCTTCGTTGTTTGGCTTCGTGATTATCGTCAGAGATGGGCAGAAAATTCTTCGTCGGCGGCAACTGGAAATGCgtatgtctccgatcgtactctttccctatctttatttttatttttctttttctttttctttttttttttctttttccctgtttggatcgttttccgattc----------------------

upper sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 1
---CTCCACGAAAACCCTCTGCCTCCTTCGCTCGCTGCACCCTCGTCTCGGCGATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc--cccccagcactagtcgtctcac-aatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcag
    ||          || ||   |||  | |  | | |        |  ||| |      |     |  || ||||| ||| ||||||||||||||||||||||| || |     || | |  ||  |   ||  | ||  ||  ||||| || |  |     |  |  || |     |  |  |   ||    |   |||                       
TTTATCTGTCGGTGGGCTGTGGA-CCTGTGGTTTCGGTATTTCATCGTTAGCGGTTTG--AAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctctgatcctcggttctgttttactttcgaagtcatcttccgaattactcattttctgt-ttggttgccaagaaaacgatggaaaaacgaatgaa---------------------

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|33692885|gb|CF321124.1|CF321124
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|88575287|gb|CI669432.1|CI669432
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|2312292|gb|C28447.1|C28447
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|25800835|gb|CA756796.1|CA756796
EST:     GGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: GGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|88391559|gb|CI600748.1|CI600748
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|88722774|gb|CI746284.1|CI746284
EST:     ATCCATCCATGGCTGCCAGGAAGTCCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|86830034|gb|CI288672.1|CI288672
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|427784|gb|D23922.1|D23922
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|33686817|gb|CF315056.1|CF315056
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAAT-GGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGC