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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcattttatttcagcaaccatttcttgaaacaaattagttctcgcttcctgattcattcatttcattattccatatcttgcttgttgatactgattttgatcatgtcatgcaaatattttcag

Basic information

species Oryza sativa
transcript LOC_Os03g55590.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55590.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G171468_T03 (Zea mays), 5'ss of exon 2
TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcattttatttcagcaaccatttcttgaaacaaattagttctcgcttcctgattcattcatttcattattccat-atcttgcttgttgatactg-attttgatcatg---tcatgcaaatatt----ttcag
                       | |||||||| || || ||||||||||||||| | || || ||||| || ||||| |||||||||||||||||||||||| ||   | |   | ||||| | |  |   | |||||||    |   |   |  | |       | |  | | | |   | |||||| ||| | |  | |||||  | || ||| |       | ||   |   ||    |||||
-----------------------TGGCTACTCCGAAACAGATCAGGGAGGTGATGCAAGTGGACGGGCTTACAAACGATGAAGTGAAAAGCCATCTCCAGgtgcgcgcgcgctt-taattttgtctagggctctatttcttcgtccctgtatatcttagt---agaactagtgcctgttccttttccatcatccttcggggtgatatggtatcttgtttggaaacttattggatcgttcgtgttcag

upper sequence: LOC_Os03g55590.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G124540_T01 (Zea mays), 5'ss of exon 4
TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcattttatttcagca--accatttcttgaaacaaattagttctcgcttcctgattcattc--atttcattattccatatcttgcttgttgatactgattt--tgatcatgtcatgcaaatattttcag
                       |||||||||| ||||| |||||||||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||||||  | ||    |||| |    |||  |  ||||| |   |  |         || | |||  ||||  |  |    || ||     |||||| || | || |||||||   |   | |||| ||    ||||| |||
-----------------------TTGCTACTCCGAAGCAGATCAGGGAGGTGATGAAGGTGGACGGGCTTACAAACGATGAAGTGAAAAGCCATCTCCAGgtgagcaatgatcc---gttttgtccgggcattattatttccttctagtagcgccgcgccggtgcctatttcagacgaaggcgatgatatagcatcttgttt-tggaaactgattcgatcggcgtgtcgtgttcgtattt-cag

upper sequence: LOC_Os03g55590.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G171468_T02 (Zea mays), 5'ss of exon 4
TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcattttatttcagcaaccatttcttgaaacaaattagttctcgcttcctgattcattcatttcattattccat-atcttgcttgttgatactg-attttgatcatg---tcatgcaaatatt----ttcag---
                       | |||||||| || || ||||||||||||||| | || || ||||| || ||||| |||||||||||||||||||||||| ||   | |   | ||||| | |  |   | |||||||    |   |   |  | |       | |  | | | |   | |||||| ||| | |  | |||||  | || ||| |       | ||   |   ||    |||||   
-----------------------TGGCTACTCCGAAACAGATCAGGGAGGTGATGCAAGTGGACGGGCTTACAAACGATGAAGTGAAAAGCCATCTCCAGgtgcgcgcgcgctt-taattttgtctagggctctatttcttcgtccctgtatatcttagt---agaactagtgcctgttccttttccatcatccttcggggtgatatggtatcttgtttggaaacttattggatcgttcgtgttcagaag

upper sequence: LOC_Os03g55590.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA07G33130.1 (Glycine max), 5'ss of exon 4
TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcattttatttcagcaaccatttcttgaaacaaattagttctcgcttcctgattcattcatttca-----ttattccatatcttgctt----------gttgatactgattttgatcatgtcat-gcaaatattttcag
                         ||||| ||||||||||| || ||| | ||| |||||||||| || || ||||| |||||||| |||||| | || |||||         ||  |||| |||  |   ||||||           ||   |   | ||| |||  |||| |    |     | |  |||  |  |  ||          |||   | |||  ||||| ||    |     ||  || |||
-----------------------CAGCTACACCAAAGCAAATTAGAGAGCTTATGCAGGTTGATGGCCTAACTAACGATGAAGTGAAGAGCCATTTACAAgtgagttcttggaacttgtttttttttggt--ccatttaactgcttgtcttttgtgatgattcatgaggcatttaaggaaaaaaatcacaccaagttgtaattatgttatgaagtttggattgagattgatgatacggtcatgtatggttgcag

upper sequence: LOC_Os03g55590.3 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S83_100V6.1 (Physcomitrella patens), 5'ss of exon 5
TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcatttt-------atttcagcaaccatt----tcttgaaacaa----------------attagttctcgcttcctgattcattcatttcattattccatatcttgcttgttgat--actgattttgatcatgtcatgcaaatattttcag
                       |||| || |||||||||||  | ||| |||||||||| || || || ||||||||||||||||| |||||||| |||||    |  |  |   ||| ||       ||   ||| |  ||     | | |  | ||                ||| | | ||  | ||   |||| |    | | |    | ||| |||| |    |   |  || || |       |   |    ||   |||
-----------------------TTGCCACGCCAAAGCAAATACGCGAGCTGATGAAGGTCGACGGCCTTACCAACGACGAAGTGAAGAGCCATCTGCAGgtatatactctacttccatattgcacaatatgcgagcgattatgaatgtttcgggataagaatccaatatatcgtattggctgtcagtgccattttcacttcgataactgcagcctatgttgcatagaaacggatggacttagtctggaacgaactgtgatgcgcag

upper sequence: LOC_Os03g55590.3 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S166_107V6.1 (Physcomitrella patens), 5'ss of exon 6
TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcattttatttcagcaaccatttcttgaaacaaattagttctcgcttcctgattcattcatttcattattccatatcttgcttgttgatactgattttgatcatgtcatgcaaatattttcag
                       |||| || || || || ||| | ||| ||||||| || ||||| ||||| |||||||||||||| || ||||| |||||  ||  | |    |  |   | |  || |  | || ||  ||     |||||  |   | ||||  |    | || || |      || ||  |  ||     |||  |||                         
-----------------------TTGCAACACCCAAACAGATCCGCGAGTTGATGAAAGTGGATGGCCTCACGAACGACGAAGTGAAGAGTCATCTGCAGgt--gctgatattgatt-tgacagtctagtattc-ttgctctaactggcttagtgtttcttccctgtctg---cgttgcagtcccaactaactcccaagtgatctctggatttag-----------------------

upper sequence: LOC_Os03g55590.3 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ15083 (Selaginella moellendorffii), 5'ss of exon 4
TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcattttatttcagcaaccatttcttgaaacaaattagttctcgcttc-ctgattcattcatttcattattccatatcttgcttgttgatactgattttgatcatgtcatgcaaatattttcag
                       |||| ||||||||||||||| | ||  | |||||||| ||||| || || ||||| ||||| |||||||| |||||||||||  |      |   ||| || ||     | |||           |||  || ||  |||  ||  |||  ||                                                               
-----------------------TTGCCACTCCAAAGCAAATCCGAGAACTCATGAAGGTAGATGGTCTTACAAACGATGAAGTAAAAAGCCACCTCCAGgtgagtga-----tccagtttcatctcgaagtcgattc---------gattgattttcttttcgttggatcaagcag--------------------------------------------------------------

upper sequence: LOC_Os03g55590.3 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ37607 (Selaginella moellendorffii), 5'ss of exon 4
TTGTTGTTCCACCATGATTGCAGTTGCTACTCCAAAGCAAATCAGGGAGGTGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaacacccctcattttatttcagcaaccatttcttgaaacaaattagttctcgcttc-ctgattcattcatttcattattccatatcttgcttgttgatactgattttgatcatgtcatgcaaatattttcag
                       |||| ||||||||||||||| | ||| | |||||||| ||||| || || ||||| ||||| |||||||| |||||||||||  | |      || ||| ||   | |  |  |||        ||||  || ||  |||  ||  |||  ||                                                               
-----------------------TTGCAACTCCAAAGCAAATCCGAGAGCTCATGAAGGTAGATGGTCTTACAAACGATGAAGTAAAAAGCCACCTCCAGgtgagtgatc------cagtttcttctcgaagtcgattc--------aattgattttcttttcgttggatcaagcag--------------------------------------------------------------

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|87026879|gb|CI259532.1|CI259532
EST:     TGATGAAGNTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29628391|gb|CB633402.1|CB633402
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|89188485|gb|CI115734.1|CI115734
EST:     GTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: GTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|86435012|gb|CI106245.1|CI106245
EST:     AAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: AAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|88990876|gb|CI108263.1|CI108263
EST:     GAAAAGCCATCTCCAG                         AAGTATCGTCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: GAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29668815|gb|CB665090.1|CB665090
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|27546309|gb|CA764507.2|CA764507
EST:     GGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: GGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29657859|gb|CB654134.1|CB654134
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29670047|gb|CB666322.1|CB666322
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|88240561|gb|CI239723.1|CI239723
EST:     AAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: AAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|86258851|gb|CI000080.1|CI000080
EST:     GGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: GGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29672537|gb|CB668812.1|CB668812
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29668893|gb|CB665168.1|CB665168
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29668892|gb|CB665167.1|CB665167
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29667571|gb|CB663846.1|CB663846
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|86260261|gb|CI066134.1|CI066134
EST:     GATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: GATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|86535219|gb|CI175425.1|CI175425
EST:     GAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: GAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
EST: gi|29644727|gb|CB649734.1|CB649734
EST:     TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAG                         AAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT
genomic: TGATGAAGGTTGATGGGCTCACCAACGACGAAGTGAAAAGCCATCTCCAGgtgagcaaac ... atattttcagAAGTATCGGCTGCACAACCGGAAATCACCAGGCACAGCTTCAGCGAGCCAT