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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaaaacttcagaaattctgctggacgctgaacatctgaactagtttctgtcgctcatattactctaaacggttgatattctcttccaacttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC

Basic information

species Oryza sativa
transcript LOC_Os03g02170.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G092776_T07 (Zea mays), 3'ss of exon 5
gtatgaaaaaacttcagaa-----attctgctggacgctgaacatctgaactagtttctgtcgctcatattactctaaacggttgatattctct-------tccaacttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
||| ||      | ||||      ||        | |||||||||||    | |  ||  | |  || | ||| | |   | || |||| ||||       | | ||  ||||||||||||||| ||||| ||||||||||| ||||||||||| |||||||| |||||||||||||||||| | ||||| ||||| |||||||||||||||||
gtaggactgcgttccagatcatgtatctaatgaaatgctgaacatct----tggcatcatttggacacactacaccaggtgattcatatgctctaattctcttcgacccgacagGTTTAGCTGCACCAGCCATTGCTGCAGGATTTGGTGCTCTAGCTCCAACACTGGGCACACTTGTCCCTTTCATAGGGGCTAGTGGATTTGCTGCTATGGC

upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G092776_T04 (Zea mays), 3'ss of exon 6
gtatgaaaaaacttcagaaattctgctggacgctgaacatctgaactagtttctgtcgctcatattactctaaacggttgatattctcttccaacttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC-----------------------------------------------------
                                                                 |  |  | | | |  | |||||||||  ||  ||||||||||||||| ||||| ||||||||||| ||||||||||| |||||||| |||||||||||||||||| | ||||| ||||| |||||||||||||||||                                                     
----------------------------------------------------------------gtgattcatatgctcta-attctcttc-gacccgacaggtttagctgcaccagccattgctgcaggatttggtgctctagctccaacactgggcacacttgtccctttcatagGGGCTAGTGGATTTGCTGCTATGGCTGCTGCGGCAGGATCTGTTGCTGGCTCTGTGGCAGTTGCTGCCTCATTTGGAG

upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G07870.1 (Glycine max), 3'ss of exon 3
gtatgaaaaaacttcagaaattctgctggacgctg-aacatctgaactagtttctgtcgctcatattactctaaacggttgatattctcttccaac--ttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
   ||  || || | |  |  | | |||    ||| || || | |  |    |  |  |    |  |  |  |   | ||| | || | ||    |  || ||||| |||||||| |||||||||||||||||| |||||||| | ||||||||| |||| || ||  | ||||| || ||||| |  | |||||||||    ||
--gtgtgaataccttaacatcttttctgtgttctggaatatataatttcaaattggatgagtttccttgttgatttgattgtttttgtttttatgcatttaacagGATTAGCTGCCCCAGCAATTGCTGCAGGGCTTGGTGCTTTGGCTCCAACCTTGGGTACTCTGATTCCTGTAATTGGAGCAAATGAATTTGCTGCAGCTGC

upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 4
gtatgaa---aaaacttcagaaattctgctggacgctgaacatctgaactagtttct-gtcgctcata---ttactctaaacggttgatattctcttc-caacttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
||||| |    | || |       | | ||    |           |  || ||||  |  |   | |   |||||  | | | ||| | || | ||  | | |  ||||| |||||||| ||||| |||||||||||  |||||||| | ||||||||  |||| || ||  ||||||| || || || || || ||||||||    ||
gtatggattggagaccttgttgtcttttctaactgtattgtggaacatataatttccagatgaataaacttttactggatatgattgtttttattttaaccattcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCTTTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGGTTTGCTGCAGCTGC

upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 4
gtatgaaaaaacttcagaaattctgctggacgctg-aacatctgaact-agtttctgtcgctcatattact--ctaaacggttgatattctcttccaacttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
||||||| |  | | |  |  | | |||    ||| || || |||  | |  ||   |   |    ||  |   | ||  |||  | || |  | ||  || ||||| |||||||| |||||||||||||||||| |||||||| | ||||||||| |||| || ||  |||| || || ||||| || |||||||||||    ||
gtatgaata--ccttaacatcttttctgtgttctggaatatatgatttcaaattggatgagtttccttgttgatttaattgtttttgtttttatgca-tttaacagGATTAGCTGCCCCAGCAATTGCTGCAGGGCTTGGTGCTTTGGCTCCAACCTTGGGTACTCTGATCCCCGTAATTGGAGCAAGTGGATTTGCTGCAGCTGC

upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgaaaa-----aacttcagaaattctgctggacgct--gaacatctgaactagtttctgtcgctcatattactc--taaacggttgatattctcttccaacttga-cagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
||||||        ||||    | ||        ||| |  ||| ||    | || | | | | |   ||  || |   ||| | |||   |||   |   |  |  | |||| || |||||||||||||| ||||||||||| |||||  | |||||||| || |||||| | || || || || ||||| || || ||||||||    ||
gtatgatgtcttctaactgttaatatctcttccaacgtttagaaaattaagagta-tgtgtttggaaaatgctaattcttaatctgttttgattacatattatgtgaaacagGATTGGCTGCTCCAGCAATAGCTGCAGGGTTCGGTGCATTGGCTCCAACTCTAGGCACAATAGTTCCGGTAATTGGAGCCAGTGGGTTTGCTGCAGCTGC

upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
gtatgaaaaaacttcagaaattctgctggacgctgaacatctgaacta--gtttctgtcgctcatattactctaaacggttgatattctcttccaactt--gacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
        || | |   |     |  |  |     ||  |||   | |  | ||| | |      | |  | |  ||  || |  |  | || ||   |   |||||||| ||||||||||||||||||||||| ||| ||||  | ||||| || || |||||| |  | || || || ||||| || || ||||| ||    ||
------gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgacttttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttctgtcgctcatattactctaaacggttgatattctcttccaacttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC
                                    ttctcttccaactt  CT-rich tract
            tcatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaaaacttcagaaattctgctggacgctgaacatctgaactagtttctgtcgctcatattactctaaacggttgatattctcttccaacttgacagGTTTAGCTGCTCCAGCAATTGCTGCAGGGTTTGGTGCTCTTGCTCCAACCCTGGGCACACTTGTCCCTGTTATAGGAGCTAGCGGATTTGCTGCTATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT