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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcacccatatttagcgataggcatgtttgttttgaatcagatcgacatgctgcagatgccacgcgtgtcttttaacaatgcgcaatcggcaatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGTGGTGGTTTCAATCCTTTTGGGG

Basic information

species Oryza sativa
transcript LOC_Os01g74580.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 9
gtcacccatatttagcgataggcatgtttgttttgaatcagatcgacatgctgcag-atgccacgcgtgtcttttaaca-atgcgcaatcggcaatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGTGGTGGTTTCAATCCTTTTGGGG---
   ||    ||||       ||  |    | | ||    |  | |    |||| |   |     |||     |||  || | ||     | |||  |  ||||| ||||| |||||||| ||||||||||| || ||||| ||||||||| | || ||||||||||||||||| || |||||    ||||||||||||||||   
-atacaatcattttttttatggttttccggctctgtga-atgttgtttcgctggaatgtattgtgcgatatgtttgtcacaagcttctgctgcatgtgtcagGTGCTTGGTGATGAAGACAAACGTGTAAGGTATGACCGTGGAGAGGATGTGGAGGAGATGAATATGGGAGGCGGGGGTGGC---TTCAATCCTTTTGGGGGAG

upper sequence: LOC_Os01g74580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv08s0040g02090.t01 (Vitis vinifera), 3'ss of exon 8
gtcacccatatttagcgataggcatgtttgttttgaatcagatcgacatgctgcagatgccacgcgtgtcttttaacaatgcgcaatcg------gcaatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGTGGTGGT---TTCAATCCTTTTGGGG
|    | |  || |   |  || |   |   |||    || | | || || |   ||    | |    | |    | |||| |||||        | ||||| |||||||||||||||||||| ||||||  |||||| ||| |||| || ||  |||| || |||  |||||| || || ||||||||    |||||||| ||||   
gatttcgaagttcatgaaatggaac--taactttatggcacagcaac-tgttattgacattaag---atatgcctaaaatgtgcaattttatattgaaatttacagGTTCTTGGGGATGAAGAAAAACGTACAAGATATGACAGAGGGGAAGACATTGAAGACATGGGTATGGGTGGTGGTGGTGGTGGCGGCTTCAATCCATTTG---
















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|29616880|gb|CB621892.1|CB621892
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88955408|gb|CI091500.1|CI091500
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|112786970|gb|EE591794.1|EE591794
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGACGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|86414025|gb|CI068232.1|CI068232
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88835888|gb|CI370993.1|CI370993
EST:     TTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: TTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|86496076|gb|CI138709.1|CI138709
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|88840222|gb|CI079676.1|CI079676
EST:     AGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTNGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: AGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|86433951|gb|CI094294.1|CI094294
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|8527566|gb|AU092381.1|AU092381
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|87021666|gb|CI276065.1|CI276065
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|5004271|gb|AU069420.1|AU069420
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|94362193|gb|CI052510.1|CI052510
EST:     GCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: GCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
EST: gi|89193984|gb|CI116421.1|CI116421
EST:     ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAG                         GTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT
genomic: ACCGAGAAGAAGCAGAAAACATGTTTCGAGAAATTGCTGCAGCTTATGAGgtatgaataa ... caatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgctgcagatgccacgcgtgtcttttaacaatgcgcaatcggcaatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGTGGTGGTTTCAATCCTTTTGGGG
                         ttttaac  putative branch site (score: 2)
                         ttttaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacccatatttagcgataggcatgtttgttttgaatcagatcgacatgctgcagatgccacgcgtgtcttttaacaatgcgcaatcggcaatttgcagGTTCTTGGGGATGAAGATAAACGTGTAAGATACGACCGAGGAGAGGATCTTGATGAGATGAATATGGGAGGAGGAGGTGGTGGTTTCAATCCTTTTGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - ggcatgt
- - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - tgctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgcg