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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatggacaggcttgtactattcactaagcttttactggattactgtctatcattgatcactcctgagatcatttcctttttttctaaatcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAGACTTGATCGTGGGCTCCTGCTTACAG

Basic information

species Oryza sativa
transcript LOC_Os03g01750.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G052546_T01 (Zea mays), 3'ss of exon 4
----tttatggacaggcttgtactatt-cactaagcttttactggattactgtctatcattgatcactcctgagat-catttcctttttttctaaatcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAGACTTGATCGTGGGCTCCTGCTTACAG
     ||     |    || |   ||| |  || ||||||| |   ||   |||||| |     |    |||| ||   |||| |||    | |  | |||  ||| |||||| ||||||||||| || || |||||||||||||||||||||||||||||||| || || ||||||||||||
tgtgcttgccatctaatttttgtgattgcgttatgcttttagtaagtt-tggtctattaa----cttatctgatatgtgtttcttttccccccatgttatta-tagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG

upper sequence: LOC_Os03g01750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 4
--tttatggacaggcttgtactattcactaagcttttactggattactgtctatcattgatcactcctgagatcatttcctttttttctaaatcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAGACTTGATCGTGGGCTCCTGCTTACAG
    | ||||    ||   |  ||     ||    | |    |||  | | |    |  || | |  ||   | |   ||||| |  | || | |||   ||| ||||| ||||| |||||  | ||||||||||| |||||||| || ||||||||||| ||||| || ||| |||||
atagtttggattaactaa-aggatcactcaattgctcatcctattcttttgttctttgaataattaatgttgttaac-cctttctaacgaagtaattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG

upper sequence: LOC_Os03g01750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G34370.1 (Glycine max), 3'ss of exon 4
--tttatggacaggcttgtactattcactaagcttttactggattactgtctatcattgatcactcctgagatcatttcctttttttctaaatcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAGACTTGATCGTGGGCTCCTGCTTACAG
    | ||||    ||   |  ||     ||    | |    |||  | | |    |  || | |  ||   | |   ||||| |  | || |  ||   ||| ||||| ||||| |||||  | ||||||||||| |||||||| || ||||||||||| ||||| || ||| |||||
atagtttggattaactaa-aggatcactcaattgctcatcctatttttttgttctttgaataattaatgttgttaac-cctttctaacgaagtgcttcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG

upper sequence: LOC_Os03g01750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 4
---tttatggacaggcttgtactattcactaagcttttactggattactgtctatcattgatcactcctgagatcatttcctttttttctaaatcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAGACTTGATCGTGGGCTCCTGCTTACAG
   || ||||  | |||  |   |          |||  || | ||  |||  ||   |      |      | |||||| || || | |   ||   |  ||| ||||| ||||| |||||||| |||||||| ||||| ||||| || ||||||||||| ||||| || ||| |||||
aacttaatgggaatgctctttaaaagtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgt---tctgatacagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAG

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|29640152|gb|CB645161.1|CB645161
EST:     GGAGAAATCCGATACGTACAGCACCAACATGACGCAAGCTATGGGAGCAG                         TGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAG
genomic: GGAGAAATCCGATACGTACAGCACCAACATGACGCAAGCTATGGGAGCAGgtaaagaccc ... tcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAG
EST: gi|29680013|gb|CB676288.1|CB676288
EST:     GGAGAAATCCGATACGTACAGCACCAACATGACGCAAGCTATGGGAGCAG                         TGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAG
genomic: GGAGAAATCCGATACGTACAGCACCAACATGACGCAAGCTATGGGAGCAGgtaaagaccc ... tcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAG
EST: gi|29641485|gb|CB646492.1|CB646492
EST:     GGAGAAATCCGATACGTACAGCACCAACATGACGCAAGCTATGGGAGCAG                         TGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAG
genomic: GGAGAAATCCGATACGTACAGCACCAACATGACGCAAGCTATGGGAGCAGgtaaagaccc ... tcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctatcattgatcactcctgagatcatttcctttttttctaaatcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAGACTTGATCGTGGGCTCCTGCTTACAG
                                      ttctaaa  putative branch site (score: 2)
                                             tcatttct  CT-rich tract
                                 tttttttctaaatcat  TA-rich tract