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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgcattttaagttgttctcatcacgtcttttactcgagtgagcatttcagctaaatgcctcgtgtgtcctgacatactattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTTTGCTGGGTCTGTCCAGACATTGTGGCCCCCCACATGGACCATTTCATGC

Basic information

species Oryza sativa
transcript LOC_Os04g59494.2
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 24
gtaattgcattttaagttgttctcatcacgtcttttactcgagtgagcatttcagctaaatgcctcgtgtgtcctgacatactattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTTTGCTGGGTCTGTCCAGACATTGTGGCCCCCCACATGGACCATTTCATGC
||   || |||||||| | |||| ||  |   ||| | |  |      |||||| ||||||| || || |  ||      ||  | |||||| ||||| ||||||||| | |||||||| || |||||||||||||||||| ||||||||||||||||||| |||||||| || ||||| ||||||||||
gtgggtg-attttaaggt-ttcttatgtcacgtttcatttaaa-----atttcaactaaatggctagttttccccccttcacattgacagGGTTTGAACAAGTCACTTGTTGAAAATAGTGCGATCACTCTTGGGAGGCTTAGCTGGGTCTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM5G869572_T01 (Zea mays), 3'ss of exon 4
gtaattgcattttaagttgttctcatcacgtcttttactcgagtgagcatttcagctaaatgcctcgtgtgtcctgacatactattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTTTGCTGGGTCTGTCCAGACATTGTGGCCCCCCACATGGACCATTTCATGC
|| | || ||||| |||   | ||||      | |||    | |||  | ||        | |  | | |  | | ||||    |  ||||| | ||| ||||||||| | ||||| ||||| |||||||||||||||||| ||||||| ||||||||||| |||||||| || ||||| ||||||||||
gtgagtg-atttttagtg--tttcatttaagatcttaactaaatgactagttttttcttcttctcccttttccttcacat----tggcagGGTTCGAACAAGTCACTTGTTGAAAACAGCGCGATCACTCTTGGGAGGCTTAGCTGGGTGTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGC

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 24
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 24
gtaattgcattttaagttgttctcatcacgtcttttactcgagtgagcatttcagctaaatgcctcgtg-tgtcctgacatactatt----acagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTTTGCTGGGTCTGTCCAGACATTGTGGCCCCCCACATGGACCATTTCATGC
                | ||| |  |   |    ||| || | |     ||||   ||  | |||  |  |    ||| ||   |||     ||||| || |||||||||||| | |||||||| || ||||| ||||||||||||   |||||||| ||||| ||||| || |  || ||||| ||||| ||||
-------------gtatcgtttttgttctgc---ttaatcaattattactttctattatcttcctgattctaatttgagatttgattttgggcagGGTTTTAATAAGTCACTTGTGGAAAATAGTGCCATCACCCTTGGGAGGCTTGCTTGGGTCTGCCCAGAGATTGTAGCACTGCATATGGAGCATTTTATGC

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 24
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 24
gtaattgcattttaagttgttctcatcacgtcttttactcgagtgagc-atttcagctaaatgcctcgtgtgtcctgacatactattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTTTGCTGGGTCTGTCCAGACATTGTGGCCCCCCACATGGACCATTTCATGC
|| ||||  || |   ||  | | |  | ||  |  | ||   |   | ||||| |  || ||  || |   |||||||  |  |   ||||   | || ||||||||  | |||||||| || ||||| ||||||||||||   |||||||||||||| |||||| | |  || ||||| ||||| ||||
gtgattgtcttgtgcatttgtgtga--atgttctggattctttttttctatttctgtaaattgtatctt---tcctgacg-atgac--cagGAGCTCAACAAGTCACTCATAGAAAATAGTGCCATCACCCTTGGGAGGCTTGCTTGGGTCTGTCCAGAAATTGTGTCACTGCATATGGAGCATTTTATGC

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|58608072|gb|CK036105.1|CK036105
EST:     TGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAG                         GGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTT
genomic: TGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAGgtaattgcat ... actattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTT
EST: gi|58671684|gb|CK060370.1|CK060370
EST:     TGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAG                         GGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTT
genomic: TGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAGgtaattgcat ... actattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTT
EST: gi|86850485|gb|CI307714.1|CI307714
EST:     TGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAG                         GGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTT
genomic: TGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAGgtaattgcat ... actattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTT
EST: gi|58592654|gb|CF990962.1|CF990962
EST:     TGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAG                         GGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTT
genomic: TGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAGgtaattgcat ... actattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactcgagtgagcatttcagctaaatgcctcgtgtgtcctgacatactattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTTTGCTGGGTCTGTCCAGACATTGTGGCCCCCCACATGGACCATTTCATGC
                                    tcctgac  putative branch site (score: 2)
                                           atactatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgcattttaagttgttctcatcacgtcttttactcgagtgagcatttcagctaaatgcctcgtgtgtcctgacatactattacagGGCTTGAATAAGTCACTTCTCGAAAATAGCGCAATCACTCTTGGGAGGCTTTGCTGGGTCTGTCCAGACATTGTGGCCCCCCACATGGACCATTTCATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA