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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatacaggctcactctgttattttgggtagttttgtgatggtgctttccaaattatctaaccgatgtgtttccagGTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGGCAGATTGTGAGATCAGATGTTGTTGGGGCACTGAAGATGCGGACATATT

Basic information

species Oryza sativa
transcript LOC_Os01g50770.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G436835_T01 (Zea mays), 3'ss of exon 5
---------------gtaagatacaggctcactctgttattttggg---tagttttgtgatggtgctttccaaattatctaaccgatgtgtttccagGTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGGCAGATTGTGAGATCAGATGTTGTTGGGGCACTGAAGATGCGGACATATT
                |    ||    |||  | | | ||   ||     || | ||||||||| |||  ||||  | |  ||   ||| | | ||||| ||||||||||| |||||||||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||||||||||||| |||||||
gtatgttgatttactatttactaagacctctatttttaatgcaggcaatcagctctgtgatggtacttgacaaaccaccacactt-tgtatgtgcagGTCTTCTTGGATGTAGTGGAGAGTGTTAACATTCTAGTTAACAGCAATGGCCAGATTGTGAGATCAGATGTGGTTGGGGCACTGAAGATGCGAACATATT

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G162145_T01 (Zea mays), 3'ss of exon 4
----------gtaagatacaggctcactctgtt-attttgggta----gttttgtgatggtgctttccaaattatctaaccgatgtgtttccagGTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGGCAGATTGTGAGATCAGATGTTGTTGGGGCACTGAAGATGCGGACATATT
           ||  ||  |   || |||| || | |   || |    ||| ||||||||  |||  ||||  | |  ||   ||| | | ||||| ||||||||||| || ||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||
gtatgttgatttactatttaccttctctctttttagtgcaggcaatcagttctgtgatggcacttgacaaaccaccacact--tgtatctacagGTCTTCTTGGATGTAGTAGAGAGTGTTAACATTCTAGTTAACAGCAATGGGCAGATTGTGAGATCAGATGTGGTTGGGGCACTGAAGATGCGAACATATT

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0225g00220.t01 (Vitis vinifera), 3'ss of exon 4
gtaagatacaggctcactctgttattttgggtagttttgtgatggtgctttccaaattatctaaccgatgtgtttccagGTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGGCAGATTGTGAGATCAGATGTTGTTGGGGCACTGAAGATGCGGACATATT
||| |  |     |   |  ||||| |      |||||       ||  |   |||   | |      ||| |   ||||| ||||||||||| ||||| |||||||| || ||||| |||||||||||||| ||  | ||||| ||||||||||| ||| |||||||| | |||||||
gtaggtcaatttttatatgagttatatattcatgttttaaaccactgtataataaagc-tttggtttttgt-tggtcagGTATTCTTGGATGTGGTGGAAAGTGTTAATATACTTGTAAACAGCAATGGGCAAATAATTAGATCGGATGTTGTTGGAGCATTGAAGATGAGAACATATT

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|163923569|gb|EG713310.1|EG713310
EST:     CAAATGCCGTGTCATGGCGGAGTGAGGGTATTCGGTACAAGAAGAATGAA                         GTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGG
genomic: CAAATGCCGTGTCATGGCGGAGTGAGGGTATTCGGTACAAGAAGAATGAAgtaagataca ... gtgtttccagGTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGG
EST: gi|33793248|gb|CF322504.1|CF322504
EST:     CAAATGCCGTGTCATGGCGGAGTGAGGGTATTCGGTACAAGAAGAATGAA                         GTGTTCTTGGATGTTGTGGGAGAGTGTTAACATTCTTGTTAACAGCAATGG
genomic: CAAATGCCGTGTCATGGCGGAGTGAGGGTATTCGGTACAAGAAGAATGAAgtaagataca ... gtgtttccagGTGTTCTTGGATGTTGTGG-AGAGTGTTAACATTCTTGTTAACAGCAATGG
EST: gi|58673470|gb|CK062156.1|CK062156
EST:     CAAATGCCGTGTCATGGCGGAGTGAGGGTATTCGGTACAAGAAGAATGAA                         GTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGG
genomic: CAAATGCCGTGTCATGGCGGAGTGAGGGTATTCGGTACAAGAAGAATGAAgtaagataca ... gtgtttccagGTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgggtagttttgtgatggtgctttccaaattatctaaccgatgtgtttccagGTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGGCAGATTGTGAGATCAGATGTTGTTGGGGCACTGAAGATGCGGACATATT
                                  atctaac  putative branch site (score: 2)
                                              tgtttcc  putative PPT
                             aaattatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatacaggctcactctgttattttgggtagttttgtgatggtgctttccaaattatctaaccgatgtgtttccagGTGTTCTTGGATGTTGTGGAGAGTGTTAACATTCTTGTTAACAGCAATGGGCAGATTGTGAGATCAGATGTTGTTGGGGCACTGAAGATGCGGACATATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG