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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgatcgagtccctaatttaatatcggtatattctgcccaaatcaaatgtcccgaatcacacgtgttaacatttttttcgaaataaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAAT

Basic information

species Oryza sativa
transcript LOC_Os06g40650.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40650.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G071659_T01 (Zea mays), 3'ss of exon 7
-----gtacttgatcgagtccct-aatttaatatcggtatattctgcccaa----atcaaatgtcccgaatc-----acacgtgttaacattt---ttttcgaaataaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAAT
     ||| || ||   | |  | ||  || ||  |     | |||  | |     || | |||| | |        ||||    |||||| |   ||||  |||||||    ||||||||||||| |||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||
gtagtgtattttatttgggctttgaaaatagtactgtgccttcctgttctaccttgtctactgtcacaataaggcaaacacagagtaacatctatcttttgtaaataaaaa--cagCCAGTTCCCCCTGTCAATTGTTCTTGTCGGGGTTGGTGATGGACCATGGGACATGATGCACCAGTTTGATGACAATATACCTGCTCGGTCATTTGACAAT

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G345544_T02 (Zea mays), 3'ss of exon 7
-----gtacttgatcgagtccct-aatttaatatcggtatattctgcccaaatcaaatgtcccgaatc-----acacgtgttaacattt--ttttcgaaataaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAAT
     |||  | || | | |  | ||  || || |   |  |||| ||    || | |||| | |        ||||    |||||| |   |||  ||| ||     ||||||||||||| |||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||
gtactgtatcttattggggctttgaaaatagtaccttcacgttctaccttg-tctactgtcacaacagggcaaacacagaataacatctaccttttaaaaaaataaaacagCCAGTTCCCCCTGTCAATTGTTCTTGTTGGGGTTGGTGATGGACCATGGGACATGATGCACCAGTTTGATGACAATATACCTGCTCGGTCATTTGACAAT

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0780g00040.t01 (Vitis vinifera), 3'ss of exon 7
gtacttgatcgagtccctaatttaatatcggtatattctgcccaaatcaaatgtcccgaatcacacgtgttaacatttttttcgaaataaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAAT
          |      || | |||  |     |||||||   |  | |  | | | ||||    | ||  | || |         ||   | | |||| | | |||| |||| || ||||| ||||| || || ||||| ||||||||  ||||||| |||||||||||||| || ||| |  |  | |||||||||
----------gttcttgtattataaagtattcctattctgta-aggtaatttatacagaatgtttcttgaaaccaatcc-------atctctctgcagCGAATACCCCCTGTCAATAGTTCTGGTTGGCGTTGGGGATGGGCCATGGGATGTGATGCAGCAGTTTGATGACAACATTCCTTCCAGGGCTTTTGACAAT

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ21520 (Selaginella moellendorffii), 3'ss of exon 6
gtacttgatcgagtccctaatttaatatcggtatattctgcccaaatcaaatgtcccgaatcacacgtgttaacattttttt-cgaaataaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAAT
                     | |||  |    | ||    ||   |    |  | ||||  || |   ||     ||  || || | |||  |||||           |||||||| ||||||||||| || || ||||| ||||||||||||||||  |||||||| || || || |||   || |  |||||||| 
--------------------gtcaatgccttcttgttaatgccttcttgttttccgcgaaaaactcaacttggtgcttgcttgcgcagTAATCTTCCA-----------TTGTCTATAGTTCTTGTTGGTGTTGGAGATGGGCCATGGGACATGATGCGACAGTTTGACGATAACATTCCTCAGCGATTGTTTGACAAC

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ27121 (Selaginella moellendorffii), 3'ss of exon 6
gtacttgatcgagtccctaatttaatatcggtatattctgcccaaatcaaatgtcccgaatcacacgtgttaacatttttttcgaaataaatttc-cagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAAT
                                              ||||      |   |    || |  ||  |    || |   |   || | |||  |  | || |||||||| ||||||||||| || || ||||| ||||||||||||||||  |||||||| || || || |||   || |  |||||||| 
---------------------------------------------gtcaatgccttcttgttttccgcgaaaaactcaacttggtgcttgcttgcgcagTAATCTTCCGTTGTCTATAGTTCTTGTTGGTGTTGGAGATGGGCCATGGGACATGATGCGACAGTTTGACGATAACATTCCTCAGCGATTGTTTGACAAC

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|116875525|gb|EC366033.1|EC366033
EST:     CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG                         CCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
genomic: CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
EST: gi|116875559|gb|EC366067.1|EC366067
EST:     CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG                         CCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
genomic: CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
EST: gi|58692386|gb|CK081073.1|CK081073
EST:     CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG                         CCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
genomic: CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
EST: gi|29618637|gb|CB623649.1|CB623649
EST:     AGTAAAAGCTAG                         CCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
genomic: AGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
EST: gi|66928286|gb|CX115134.1|CX115134
EST:     CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG                         CCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
genomic: CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
EST: gi|29632713|gb|CB637722.1|CB637722
EST:     CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG                         ----TTCCCCTTGTCTATTGTTCTTGTTGGGGTGNGGTGATGGACCATGGG
genomic: CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTG-GGTGATGGACCATGGG
EST: gi|300216150|gb|HO087935.1|HO087935
EST:     CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG                         CCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
genomic: CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
EST: gi|58695004|gb|CK083691.1|CK083691
EST:     CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG                         CCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
genomic: CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
EST: gi|125863438|gb|EL586714.1|EL586714
EST:     CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG                         CCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA
genomic: CAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAGgtacttgatc ... aaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcaaatgtcccgaatcacacgtgttaacatttttttcgaaataaatttccagCCAGTTCCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAAT
                        tgttaac  putative branch site (score: 2)
                                                tttcc  putative PPT
                        tgttaacatttttttc  TA-rich tract