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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaacatttctaaatgagctttttggacatttaaattgaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG

Basic information

species Oryza sativa
transcript LOC_Os01g34620.7
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34620.9 (Oryza sativa), 3'ss of exon 3
lower sequence: AC208327.4_FGT002 (Zea mays), 3'ss of exon 4
gtattaacatttctaaatgagctttttggacatttaaatt-------gaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG
||||| ||||    | ||||| ||   | | ||||| |||       |||| || ||  |||||| ||| ||||||||  | | ||  ||  |||||||| | |     ||    || ||  |  |  ||| || |||||||||||||||||||||||||| |||||||||||||||||| ||||||  |||| | |||||| ||||||||  |||| ||||  ||| |  |||||||||
gtatttacatgcggagatgagattcaagaatatttatattaaacattgaagcacctaacttgtggtaaaactaggcataacctgaatcttattgatgtatctttttagcttcc--attctttcataccattttttggcagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTTCAGCAATATG

upper sequence: LOC_Os01g34620.9 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 3
gtattaacatttctaaatgagctttttggacatttaaatt-------gaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG
||||| ||||    | ||||| ||   | | ||||| |||       |||| || ||  |||||  ||| ||||||||  | | ||| ||  |||||||| | |   |  ||  |   || | |   | ||  | || ||||||||||||||||||||||| |||||||||||||||||| ||||||  |||| | |||||| ||||||||  |||| ||||  ||| || |||||||||
gtatttacatgcagagatgagattcaagaatatttatattaaacattgaagcacctaacttgtgataaaactaggcataacctgaagcttattgatgtatcttt-ttagctgccatctcttcttatcattttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATG
















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|218483000|gb|FG956128.1|FG956128
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|218500313|gb|FG954965.1|FG954965
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|58675402|gb|CK064089.1|CK064089
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|38482485|gb|CF966520.1|CF966520
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|38478580|gb|CF962713.1|CF962713
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|86901749|gb|CI310511.1|CI310511
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|88427128|gb|CI586676.1|CI586676
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|33808808|gb|CF330289.1|CF330289
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|38477159|gb|CF961292.1|CF961292
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|88316503|gb|CI622749.1|CI622749
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG
                         tgttaat  putative branch site (score: 3)
                      atttgttaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaacatttctaaatgagctttttggacatttaaattgaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA