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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttgttctcaatttgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagagagttcagtttcaaattagctgattttatgtttctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC

Basic information

species Oryza sativa
transcript LOC_Os09g38420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G156565_T01 (Zea mays), 3'ss of exon 4
gtatgtcttgttctcaatttgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagaga--gttcagtttca----aattagctgattttatgttt-ctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC
                                             |  |  |||| | |   |  ||| | | ||   ||| || || | |    ||| || | || |   ||  |||       |||||| | |||| |||||  || |||||||||||||||||||||||||  ||||||||||| |||||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||| |
--------------------------------------------gtacaagatgt-cccaaatcttattatgcaacacttttttgtattct----attcctgtggaaatgatttcgttcagcagcaattagtttatttcatgttaactgcagGCTGCAAAAGATGGGGAGCCATGGTGGGATAGCCCATGGGGCCCAGGAAGGCCAGGATGGCACATAGAATGCAGTGCCATGAGTGCACATTATTTGGGTC

upper sequence: LOC_Os09g38420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G002851_T01 (Zea mays), 3'ss of exon 4
gtatgtcttgttctcaatttgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagagagttcagtttca----aattagctgattttatgttt-ctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC
                                        ||  | |  |     |         |   || |    |    ||||   ||| |  | | |  | |   || ||||  |    |||||| | |||| |  ||  || ||||| |||||||||||||||||||  ||||||||||| |||||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||| |
----------------------------------------gtacaaccgtacaagatatcccaaatgctagtatgcaacaccttttgtattctatttctgtggaaatgatttagttcaatagcaattagtt-atttcacattgactgcagGCCGCAAAAGATGGGGAGCCATGGTGGGATAGCCCATGGGGCCCAGGAAGGCCAGGATGGCACATAGAATGCAGTGCCATGAGTGCACATTATTTGGGTC

upper sequence: LOC_Os09g38420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G06910.1 (Glycine max), 3'ss of exon 4
gtatgtcttgttctca-atttgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagagagttcagtttcaaatta--gctgatttt--atgtt--tctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC
||||    | |    |    |   |||  |    |||| ||   ||| | | || |  |  | |  ||  |   ||| ||| ||| || | |  | |  |||| |   |||||||     | | |  |  |||| |  ||| |  ||| ||| |||||||    |||||||||| |||||| || || ||||| |||||||| || || ||||| || ||||||||||| |||||||||  |||  | ||  
gtataatatatcagtatgaataatgataacacaaatttgttaaatatgt-tgatttcattatatattacaaaccaatgatt-attatattcttgaaa--tcttaatttagttcagaacttactcaatgtggattcttgatgctattctgcagTCTGCAAAGCCAGGGGAGCCATTTTGGGAGAGTCCCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT

upper sequence: LOC_Os09g38420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G06990.1 (Glycine max), 3'ss of exon 4
gtatgtcttgttctcaatt-tgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagagagttcagtttcaaattagctgatttt--atgtt--tctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC
||||      |    | |  |   |||  |    |||| ||    || | | || |  |  | |  ||  |  |||| ||| ||| || | |  | || |   || ||  |  |  ||       |  |||||   ||| |  ||| ||| |||||||    |||||||||| |||||| || |  ||||| |||||||| || || ||||| || ||||||||||| |||||||||  |||  | ||  
gtataatacatcagtactaataatgataacacggatttgttaaacatgt-tgatttcattatatattacaaataaatgatt-attatattcttgaaatcttaatatagtttggaacttacttaaggtggatttccaatgctattctgcagTCTGCAAAGCCGGGGGAGCCATTTTGGGAGAGTCGCTGGGGTCCTGGAAGACCTGGGTGGCATATTGAATGCAGTGCCATGAGTGCAGCTTATCTTGGTT

upper sequence: LOC_Os09g38420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G31170.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtcttgttctcaatttgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagagagttcagtttcaaattagctgattttatgtttctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC
                                                     |||| ||| ||     ||  |  | ||     ||  || || | || ||||   | || ||| | |||  |  |   |  || |||   |||||||||||||| ||||| || | |||||| || || |||||    |||||||| || ||||||||||| |||||||| ||||| ||   |||  | ||  
-----------------------------------------------------gtacgcttttt-----agttacgttttagccctacattgaatacttgtttactcatttaagtcttaaaagactt--ctgaatttttgggcagGCTGCAAAAGAAGGGGAACCCTTTTGGGAGAGTCCGTGGGGAAGAGGAAGGCCCGGTTGGCACATAGAGTGCAGTGCGATGAGCGCGGCTTATCTCGGTT

upper sequence: LOC_Os09g38420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S504_12V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgtcttgttctcaatttgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagagagtt---cagtttcaaattagctgattttatgtttctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC
||    |    |   || | ||         || || | | ||  |   ||| || ||   |   ||     ||  |  |  |  |||  |     ||  ||   | | ||   |  | | ||  | |||| | | || ||    |||  ||| |||   || |||||  ||||||| || |||||||| |||||  | || || |||||||| ||||||||||||||||||||  |  | || || |
gt-cagcgcccttgaaaatggtgagagaaaactcttctgtctgc-tgagttaggtcctagggaattagactaaatcttgtcctactaaagtgggtgttggttctcaaattttctctctctgaaggtcgctggtatcattttctcgcagAGTGCGAAACCCGGAGAGCCTGCTTGGGACAGTCCTTGGGGTCCTGGGCGCCCGGGCTGGCACATTGAATGCAGTGCTATGAGTGCGGAGCATTTAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagatttctttagagagttcagtttcaaattagctgattttatgtttctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC
                                 agctgat  putative branch site (score: 4)
                                       ttttatgtttctcc  CT-rich tract
                                      attttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcttgttctcaatttgtagatttcttctattttttgtgtatctattatgtactcttgttctatgaggaaattatttattttaatttcaagatttctttagagagttcagtttcaaattagctgattttatgtttctccagGCTGCAAAAGATGGGGAGCCATCTTGGGATAGCCCTTGGGGCCCTGGAAGGCCAGGATGGCACATAGAATGCAGTGCTATGAGTGCACATTACTTGGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG