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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatagaatttgggtactataactataagtggggtgattaccgctaacactattggtttctcctgcatataaatacttactgtcaatgcctcatggtgtagGGCCGGATCCTTGTATTTGCAGTTGAAGATGGCAGACTGCAATTAATTGTAGAGAAAGAAACTAAAGGAGCTGTCTATTCGCTGAATGCATTCAACGGAA

Basic information

species Oryza sativa
transcript LOC_Os05g51480.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------gatagaatttgggtactata-actataagtggggtgattacc--gctaacactattggtttctcctgcatataaatacttactgtcaatgcctcatggtgtagGGCCGGATCCTTGTATTTGCAGTTGAAGATGGCAGACTGCAATTAATTGTAGAGAAAGAAACTAAAGGAGCTGTCTATTCGCTGAATGCATTCAACGGAA
                                                  ||  | |||   | | || |   |   |  | | ||| |   |  | |  | |   |||||| |||| | ||||  ||| ||| |  |   |||  |||||||||| |||||||||||||||||||||||||| ||  ||||||||||||| ||||||||||| |||||||| || |||||| ||||||||||||| || |
gtgatatatctgaaatcatgatcttttactaatgctagttaactcgtttttaatacttgttcaatttacagcttgttttagttaatttctcagtgagccttttctatttctcgtgcaca-aaatggtta-tgt-atcggtacatcttgtagGGCCGAATCCTTGTATTTGCAGTTGAAGATGGAAGTTTGCAATTAATTGTGGAGAAAGAAACCAAAGGAGCAGTTTATTCGTTGAATGCATTCAATGGGA

upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 17
-------------------------------------------------------------------------------gatagaatttgggtactataactataagtggggtgattacc-gctaacactattggtttctcctgcatataaatacttactgtcaatgcctcatggtgtagGGCCGGATCCTTGTATTTGCAGTTGAAGATGGCAGACTGCAATTAATTGTAGAGAAAGAAACTAAAGGAGCTGTCTATTCGCTGAATGCATTCAACGGAA
                                                                                 ||  | |||   | | | |||    || |  |  ||  | |  |||  | |   |||||| |||| | |||| |||| |||   || | |||  ||||||||||||| ||||||||||||||||||||||| ||  ||||||| || || ||||||||||| |||||||| || |||||||||||||||||||| || |
gtagtttatctgaaagcatgatgtttcactaatactagtcagttcccttttaatacgctaaaatactggttaactcccttttaatacttgtccaat-ttactgcttgtagtttatttctctgtgaaccttgtctatttctcgtgcaca-aaatgctta-tgt-gttggcacatcttgtagGGCCGGATTCTTGTATTTGCAGTTGAAGATGGAAGCTTGCAATTGATCGTGGAGAAAGAAACCAAAGGAGCAGTTTATTCGCTGAATGCATTCAATGGGA

upper sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 5
gatagaatttgggtactataactataagtggggtgattaccgctaacactattggtttctcctgcatataaatacttactgtcaatgcctcatggtgtagGGCCGGATCCTTGTATTTGCAGTTGAAGATGGCAGACTGCAATTAATTGTAGAGAAAGAAACTAAAGGAGCTGTCTATTCGCTGAATGCATTCAACGGAA
     || ||| | | | |   | |     |  |  ||   |  ||  ||  || | ||  |||| |       | |  | | ||  |       |||||||  | || ||||| ||||| ||||||||||| | ||| ||| ||||||  |||||||| || ||||||||||| ||||   |||  ||||| || || |
---gtaagttgagaaatttgtattttttcagcattgttctagtcaaagcttctgatatc--ctgcttcctttggcct--ttttaaaac------atgtagGGAAGAATTCTTGTTTTTGCTGTTGAAGATGGAAAACTACAACTAATTGCCGAGAAAGAGACAAAAGGAGCTGTTTATTGCTTGATGGCATTTAATGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactattggtttctcctgcatataaatacttactgtcaatgcctcatggtgtagGGCCGGATCCTTGTATTTGCAGTTGAAGATGGCAGACTGCAATTAATTGTAGAGAAAGAAACTAAAGGAGCTGTCTATTCGCTGAATGCATTCAACGGAA
                           tacttac  putative branch site (score: 1)
                    atataaatacttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatagaatttgggtactataactataagtggggtgattaccgctaacactattggtttctcctgcatataaatacttactgtcaatgcctcatggtgtagGGCCGGATCCTTGTATTTGCAGTTGAAGATGGCAGACTGCAATTAATTGTAGAGAAAGAAACTAAAGGAGCTGTCTATTCGCTGAATGCATTCAACGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT