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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGCGATCGTCGCCGAGAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcctaccctcttctgtgcggttagaactagcttgtgtggttgatgcgatttgctcggtctgtgcctgagatgcgatggtttaggtccgattcat...

Basic information

species Oryza sativa
transcript LOC_Os03g03920.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G127101_T01 (Zea mays), 5'ss of exon 1
AAGGCGATCGTCGCCGAGAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcctaccctcttctgtgcggtta-gaactagcttgtgtggttgatgcgatttgctcggtctgtgcc-tgagatgcgatggtttaggtccgattcat-
||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| | |||   ||     |     |  ||| | |  |||||   || | ||| | ||   |  ||  || | || | | | || |||  |       
AAGGCGATCGTCGCCCACAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctttcccctatcatcctgagagtgctctacccttggtggt--gtgtggttt-cccgtgttacgctgtgggctgtggtcgatttggttagtcatgcg

upper sequence: LOC_Os03g03920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G057158_T01 (Zea mays), 5'ss of exon 1
AAGGCGATCGTCGCCGAGAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcctaccctcttctgtgcggttagaactagcttgtgtggttgatgcgatttgctcggtctgtgcctgagatgcgatggtttaggtccgattcat-
||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |  ||    |  ||  ||  |  ||| |    |||        | ||| | | || |     || |  ||| | | || |||  |   |   
AAGGCGATCGTAGCCGATAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctttgccctacccctg-agtgcgttctacccgtggtgtggcgcctggtttcccctgttttgctgtgggccgcggtcgatttggttagtcacgcg

upper sequence: LOC_Os03g03920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv04s0210g00220.t01 (Vitis vinifera), 5'ss of exon 1
AAGGCGATCGTCGCCGAGAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgt-gcctaccctcttctgtgcggttagaactagcttgtgtggttgatgcgatttgctcggtctgtgcctgagatgcgatggtttaggtccgattcat-
|| ||  |  || |  ||| ||||||  | || |||  |||||||||  |||| |||||||| ||||||||||||||||| ||||||||||  ||||||||||  | | |    || | |  |||  |     |   ||  |||  | | |     | |    |   |  | |  |||   | | ||| | |  | | | | 
AAAGCCGTTCTCTCGCAGAACTGCGATATTCCCGCGGAGCAGCAGCGATTGATTTACAAGGGACGGATCTTGAAGGACGACCAAACCCTAGAGAGCTACGgtatattgacatttctatccattgctctccacgcagtctgttgttatgggtagttgtagtattgaaagaacttc-gatttaa-gtttttgtttggttgcgtc

upper sequence: LOC_Os03g03920.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv03s0038g03680.t01 (Vitis vinifera), 5'ss of exon 1
AAGGCGATCGTCGCCGAGAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacg---tgcctaccctcttctgtgcggttagaactagcttgtgtggttgatgcgatttgctcggtctgtgcctgagatgcgatggtttaggtccgattcat
|||||  |  | ||  ||| |||||| || ||  |    ||||||||| |||| || ||||| ||||||||||| ||||| ||||||||||  ||||| ||||||   |   |   |||| | ||     | |    |  ||  |   ||  |    |||  |   | |  |   |   |  |||    ||||    | |   
AAGGCTCTTCTGGCGCAGAACTGCGATGTTCCATCTGATCAGCAGCGGTTGATTTATAAGGGTCGGATCTTGAAAGACGACCAAACCCTAGAGAGCTATGgtacgccgtcgttgtactctcccgtatacgtggtttgatttttggaaattttttttcttttttaattttagg---ggagtttgatttcgtagggtgaaattga

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|29616125|gb|CB621137.1|CB621137
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|88402341|gb|CI596202.1|CI596202
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCTAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTG
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTG
EST: gi|29672913|gb|CB669188.1|CB669188
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTATCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|29662282|gb|CB658557.1|CB658557
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|218503059|gb|FG958652.1|FG958652
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|88732498|gb|CI755675.1|CI755675
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|58680438|gb|CK069125.1|CK069125
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|58672635|gb|CK061321.1|CK061321
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|66932287|gb|CX119135.1|CX119135
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|58606989|gb|CK035022.1|CK035022
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|58600000|gb|CK010528.1|CK010528
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|29678485|gb|CB674760.1|CB674760
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|88356760|gb|CI619246.1|CI619246
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
EST: gi|13447548|gb|AU181042.1|AU181042
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATTGGTCCGTGGTGCTGCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACAT-GGTCCGTGGTGCTGCACCAC
EST: gi|29673316|gb|CB669591.1|CB669591
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcct ... cctcttgaagGTGTTGAGACGGATCACACCATTCACATGGTCCGTGGTGCTGCACCACCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGCGATCGTCGCCGAGAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtacgtgcctaccctcttctgtgcggttagaactagcttgtgtggttgatgcgatttgctcggtctgtgcctgagatgcgatggtttaggtccgattcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG