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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTATACAGGACCACCACGCAATCTTTCGCCTCCCTGGAGGCCAGATGACAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttccacaactcagtattatttattgcatagggttattgtttttgtttgcatttctgatcgcttgcttggttagactgttaaactgtttttcttc...

Basic information

species Oryza sativa
transcript LOC_Os01g62080.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62080.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 2
TATTATACAGGACCACCACGCAATCTTTCGCCTCCCTGGAGGCCAGATGACAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttccacaactcagt-attattta----ttgcatagggtta-ttgtttttgtttgcatttctga-tcgcttgcttggttagactgttaaactgtttttcttc
||||| || || || ||||| ||| |||||||||| ||||| ||||||||||||||||||||||||||||| || ||||| ||||| || |||||||||||||| |||| ||||||| | || ||||| |||||| |||| ||||||||||| |||| ||||| | | ||| || | | | | || ||
TATTACACCGGGCCGCCACGGAATATTTCGCCTCCTTGGAGACCAGATGACAAGGATGGACACTATGTTTTTGCGGTTGGAGAGAATCTCACACCAAGATgtatatttctccaactcaatgatcatttactccttgcattaggttgcttgtttttgttggcatctctgaatagtttgtttagatgtatt-ttcttttgaag------
















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|58593612|gb|CF991920.1|CF991920
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG
EST: gi|58680098|gb|CK068785.1|CK068785
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG
EST: gi|117243444|gb|CT848361.1|CT848361
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG
EST: gi|58694718|gb|CK083405.1|CK083405
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG
EST: gi|58654607|gb|CK043287.1|CK043287
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG
EST: gi|29665089|gb|CB661364.1|CB661364
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG
EST: gi|58691283|gb|CK079970.1|CK079970
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG
EST: gi|58593129|gb|CF991437.1|CF991437
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG
EST: gi|29679261|gb|CB675536.1|CB675536
EST:     CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGAT                         ATAGAATACTTAGCAAGATGGGTGAAG
genomic: CAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 65 (downstream exon)
Score: 60

TATTATACAGGACCACCACGCAATCTTTCGCCTCCCTGGAGGCCAGATGACAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttcc ... ggctttgcagATAGAATACTTAGCAAGATGGGTGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTATACAGGACCACCACGCAATCTTTCGCCTCCCTGGAGGCCAGATGACAAGGATGGACACTATGTTTTCGCAGTTGGGGAGAACCTTACACCAAGATgtatttttccacaactcagtattatttattgcatagggttattgtttttgtttgcatttctgatcgcttgcttggttagactgttaaactgtttttcttc

- - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA