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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcctagttggctagttcttaacttgctatcctggaattggctactgtttgtctttacatactttgggttgtgtaatcctaaactgttaacatgtgatatgatacttcttagGTGGCACGAGATGAAGACCTTGCAGAGCAGATTGGAAAGGATATATATTTTGATCTTGTAGACCATGACAAAGTGAGGAGTTTCCGTGTCCAAAAACAGA

Basic information

species Glycine max
transcript GLYMA02G43930.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 14
gttcctagttggctagttcttaacttgctatcctggaattggctactgtttgtctttacatactttgggttgtgtaatcctaaactgttaacatgtgatatgatacttcttagGTGGCACGAGATGAAGACCTTGCAGAGCAGATTGGAAAGGATATATATTTTGATCTTGTAGACCATGACAAAGTGAGGAGTTTCCGTGTCCAAAAACAGA
                   ||| ||   |||      ||  | |||   || |||  | || ||          | || |||     |   ||  |  |     | ||  ||||| || ||||||   ||  |||||||||| ||||||||  ||||||||||||||||||| ||  |||||||  |    ||  | || |  |  |||||  
-----------------gtttacctctttattt---gatacgttaca--ttatctgaaaatgct---------atcattctagttgctcctcacttagtgcttcattttctagGTTGCCCGAGATTCTGATTTTGCAGAGCAAATTGGAAAACATATATATTTTGATCTTGTGGATTATGACAACATCCAAAGCCTTCGGGCACCTAAACATT

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 10
gttcctagttggctagttcttaacttgctatcctgga-attggctactgtttgtctttacatactttg-ggttgtgtaatcctaaactgttaacatgtgatatgatacttcttagGTGGCACGAGATGAAGACCTTGCAGAGCAGATTGGAAAGGATATATATTTTGATCTTGTAGACCATGACAAAGTGAGGAGTTTCCGTGTCCAAAAACAGA
           |  ||    | |||  ||||  ||   ||    |  | |  ||||  |    || || |  | |||  ||  | | || |    |  || |  |||  ||| ||||||| ||||||||  |  |    ||||| ||||| ||||||||||||||||| || || |||||||| |||||  | || |||||  | || || ||| 
-----------gtcagcatctgact-actattatgttcatcacttcatctcagtctggaacctctctgtgaatctgtt-tctcatagtgctctgtttggaca-aatatatct-agGTGGCTCGAGATGAGAATTTGAAGGAGCAAATTGGCAAGGATATATATTTTGACCTGGTGGACCATGAAAAAGTTCGTAGCTTCCGAATTCAGAAGCAGT

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 14
gttcctagttggctagttcttaacttgctatcctggaattggctactgtttgtctttacatactttgggttgtgtaatcctaaactgttaacatgtgatatgatacttcttagGTGGCACGAGATGAAGACCTTGCAGAGCAGATTGGAAAGGATATATATTTTGATCTTGTAGACCATGACAAAGTGAGGAGTTTCCGTGTCCAAAAACAGA
          | || | |   ||| || | |  |   | ||| |  |   | || ||    |||||   || | ||||      ||      |||||  |||    | | ||||| || |||||||| ||  |    || |||||||| ||| |||||||||||||||| || |||||||| || ||  | || |||||  | || || ||  
----------gtctggataagaacctgttttagttttaatggtt--taaatctcattgtgaactttt--ttttataat----ggct------atgtgcaatg----tccctagGTTGCCCGAGATGAGGATTTGAAGGAACAGATTGGTAAGAATATATATTTTGATCTGGTGGACCATGAAAAGGTTCGCAGCTTCCGCATACAGAAGCAAC

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 14
-------------------------------gttcctagttggctagttcttaacttgctatcctggaattggctactgtttgtctttacatactttgggttgtgt-aatcctaaactgttaacatgtgatatgatacttct-tagGTGGCACGAGATGAAGACCTTGCAGAGCAGATTGGAAAGGATATATATTTTGATCTTGTAGACCATGACAAAGTGAGGAGTTTCCGTGTCCAAAAACAGA
                                || ||  |||   | |  |||        || |||    || | || ||         |  ||   |  || ||  | |  |   | || |    | || |||  ||||| ||||| ||||||||||| ||||||| ||| || ||||||| ||||||||||||||||||||| || ||||||||||| || ||||| ||| |||| || ||||
gttactagttctaatttttcttctattgacaattgctttttgaaca-tatttagtccctattcatggttgaggatgcttttgagacaattagtctccagtctgagttgagcagactttattgaacaattatttgaagcttctatagGTTGCACGAGATGATGACCTTGTAGAACATATTGGAAGGGATATATATTTTGATCTTGTGGATCATGACAAAGTTAGAAGTTTTCGTATCCAGAAGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catactttgggttgtgtaatcctaaactgttaacatgtgatatgatacttcttagGTGGCACGAGATGAAGACCTTGCAGAGCAGATTGGAAAGGATATATATTTTGATCTTGTAGACCATGACAAAGTGAGGAGTTTCCGTGTCCAAAAACAGA
                           tgttaac  putative branch site (score: 2)
                                             tacttctt  putative PPT
                                       atatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcctagttggctagttcttaacttgctatcctggaattggctactgtttgtctttacatactttgggttgtgtaatcctaaactgttaacatgtgatatgatacttcttagGTGGCACGAGATGAAGACCTTGCAGAGCAGATTGGAAAGGATATATATTTTGATCTTGTAGACCATGACAAAGTGAGGAGTTTCCGTGTCCAAAAACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG