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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgctgcggccttcaggccgtaggcgcgggttagcagttgctgcgaccttctgtttggtagatcgctgggggctcttggcgtttgatgaatgatttcttcgccgtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT

Basic information

species Oryza sativa
transcript LOC_Os01g34620.1
intron # 1
splice site 3'
intron type U2

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|218500313|gb|FG954965.1|FG954965
EST:     GCCGGCGGCGCCTCCGACCACCGCAGGGCTCCTGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
genomic: GCCGGCGGCGCCTCCGACCACCGCAGGGCTCC-GTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|218483000|gb|FG956128.1|FG956128
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGACGACCGCCTTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|38482485|gb|CF966520.1|CF966520
EST:     CGCCGGCGG-GCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCTTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|38478580|gb|CF962713.1|CF962713
EST:     CGGCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCTTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCTTTTTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|58590633|gb|CF988941.1|CF988941
EST:     CGCCGGCGGTGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCTTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCTTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCTTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|86901749|gb|CI310511.1|CI310511
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCC--                         ---AGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|88427128|gb|CI586676.1|CI586676
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|33808808|gb|CF330289.1|CF330289
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|66921894|gb|CX108742.1|CX108742
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         G-TAGTCATGGCGAGAT-GATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
EST: gi|88316503|gb|CI622749.1|CI622749
EST:     CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAG                         GGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG
genomic: CGCCGGCGGCGCCTCCGACCACCGCAGGGCTCCGTCCCGCCGCCTCCCAGgtacttgctg ... gtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatcgctgggggctcttggcgtttgatgaatgatttcttcgccgtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT
                      gtttgat  putative branch site (score: 5)
                              aatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgctgcggccttcaggccgtaggcgcgggttagcagttgctgcgaccttctgtttggtagatcgctgggggctcttggcgtttgatgaatgatttcttcgccgtcgctgcagGGTAGTCATGGCGAGATTGATGTCGTCCGCCCTCATCAGGGGTCTCGTGAGATCGAGCTGCTCGCCGACCGTAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT