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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcagaatataaataattgaatacggtcaaatgtgcagctaactaattatcatgaaatgccatcaatatgtttaaagacttacatagttacgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTGAAACGACATGTGGATCTTTGCTGCAGCAACTTCAG

Basic information

species Oryza sativa
transcript LOC_Os06g40840.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G112337_T04 (Zea mays), 3'ss of exon 1
ttcagaatataaataattgaatacggtcaaatgtgcagctaactaattatcatgaaatgccatcaa-tatgtttaaagacttaca-tagttacgttta-----gcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTGAAACGACATGTGGATCTTTGCTGCAGCAACTTCAG
       | |       || ||   ||||||  | ||  |  |  ||   | |  | |  ||  || ||  |  |||     | | | |||| ||||      ||||| || ||||  | ||||||||||||||| ||||| ||||| ||| ||||||||||||||||||| |||||||||||||||||||||
-------ttttctgccctgtatgttgtcaaaaatacatatgtcatatatacttagattcacactaaataaatgcaaatgtaaataatcgttatgtttctccatgcagGCTGCTGAGTGAAAATGGGAGTGGCAGGTCACAACGATCCATTGTTAGGTGAAACGACATGTGGGTCTTTGCTGCAGCAACTTCAG
















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|88733536|gb|CI756713.1|CI756713
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88343226|gb|CI627186.1|CI627186
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88732075|gb|CI757252.1|CI757252
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88393215|gb|CI616699.1|CI616699
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGGACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCAAAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88363588|gb|CI618149.1|CI618149
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGGACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88694716|gb|CI738754.1|CI738754
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|95100601|gb|CI692304.1|CI692304
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88576964|gb|CI673507.1|CI673507
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88761027|gb|CI770583.1|CI770583
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88827256|gb|CI777821.1|CI777821
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88404901|gb|CI685335.1|CI685335
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88393688|gb|CI621183.1|CI621183
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88386526|gb|CI575304.1|CI575304
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88577500|gb|CI674092.1|CI674092
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88590104|gb|CI708933.1|CI708933
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88381767|gb|CI682440.1|CI682440
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88394161|gb|CI684833.1|CI684833
EST:     GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
EST: gi|88315674|gb|CI615546.1|CI615546
EST:     GAGAACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAG                         GTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG
genomic: GAGCACGAAAGCCCTAGCGCGCCGCCCCCTGCACCGGGTGGGTTCCCCAGgtgagcactc ... cgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatcatgaaatgccatcaatatgtttaaagacttacatagttacgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTGAAACGACATGTGGATCTTTGCTGCAGCAACTTCAG
                               gacttac  putative branch site (score: 2)
                atcaatatgtttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcagaatataaataattgaatacggtcaaatgtgcagctaactaattatcatgaaatgccatcaatatgtttaaagacttacatagttacgtttagcagGTTGTTGAGCTAGAATGGGAGTGGCAGGGCACAATGATCCTTTGATAGGTGAAACGACATGTGGATCTTTGCTGCAGCAACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - gtgcagc
- - - - - - - - - - - - - - - - - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttacat