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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

Basic information

species Glycine max
transcript GLYMA20G02880.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaa---gtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
      | || |    ||    ||    ||| || | ||  |||   | ||  || | | || ||||  |  |||       |    | ||||||| | || ||||| |||||||| || ||||| ||||||||||| |||||||| || ||  | ||||| || ||  | ||||||||||||||||| |||
-----gtatgctattgataccctta---ttatctttagagatatcactcaatcatgtat-ataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||||| |    || |  | |   | | |  || |    ||  |      ||| ||   |  | ||  ||     ||||| ||  | ||||||  | || || || |||||||||||||| || || ||||||||||| ||||| || ||||| ||||| |||||  | ||||| |||||||||||||||
gtatgctaaaattac--tcttcctcattacaaatagtaatccac-----aaacatccctatttac-tacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G308570_T02 (Zea mays), 3'ss of exon 13
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||||| |    || |  ||  |   | |  || |    ||  |      ||| ||   |  | ||  |      ||||| ||  | ||||||  | || || || |||||||||||||| || || ||||||||||| || || || ||||| ||||| |||||  | ||||| |||||||||||||||
gtatgctaaaattactcttcatc--actgcaaatagtaatccac-----aaacatgcctacttac-tataccttaaaaggggtgtgcagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGCGCAATCTTCCTGGCTGCGAAGTTTCTTAAAGTCAAGCTTCCATCAGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 4
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||||| |   | | |  ||  | |   || || |  |  || |   ||    | ||| | |  ||||  |   |    |     | ||| ||| | || ||||| |||||||||||  |||| ||||||||||| |||||||| || ||  | ||||| || ||  | ||||||||||||||||| |||
gtatgctagtgctacccttactgtcgtttgaaattgcagttcacagttg---tgtatct-actacac-ttaatattgtgcactgtacagACTGCGTACTTCGCTTTGCCTGCAATTCGAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgatttggttgcaatttgtt-tgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||| | |   |    | ||  || | ||  |  |  |   | ||| |      ||| || |    || ||     ||||||||||| ||| ||  ||||||| |||||||||||||||||||| |||||||||||||| ||||| || || ||||| ||||||||| | ||||||||| | |||||||||
gtacgttcaagaactatttccttctaaagcttccaataattctatgtgccttgtattttcgtcttcatac-aatgaaaagtggcttgcagTCTACGGACATCTCTCTGCCTGCAATTTAAGCCTCATCATATTGCGGCTGGTGCAATATTTCTTGCGGCCAAGTTCCTTAAAGTGAAGTTACCATCAGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||| | |     |    ||  ||  ||  |     | ||| ||| | |    ||| ||      || ||    ||||  || ||| ||| ||| |||| || |||||||||||||||||||| || || |||||||| || || ||||| |||||||| |||||| | ||||||||  | |||||||||
gtacgttaaaagtctgtttccttgaaagcttcagatagatctatctgtcttgtattttcttcttcatacaatgaaaagatg-cttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 4
-------------------gtatgatt-tggttgcaatttgtttgaatttaactg---tcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
                     |||  | |  ||     | |||  | || || ||   ||  ||  | | |      | ||   ||||||||||||   ||| ||||| ||||||||||||||| ||||||||||||||||||||  | || ||||| |||||||||||||||||||||||||||||  | ||||||||||||||||| |||
gtatgattaagatgctttttcatgtctctcttttttgatagttccatttcaaatggtctctcttcctctctttctcttcttcactcacacactgga---aagcggcttgcagGCTGAGGACATCACTCTGCCTGCAATTTAAGCCCGACCACATTGCAGCAGGTGCCATTTTCCTTGCTGCCAAGTTTCTCAAAGTGAAGCTTCCATCGGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S264_33V6.3 (Physcomitrella patens), 3'ss of exon 5
---------------gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
               ||| | | |  || ||    |      |||||    |   |   ||  ||   | | | | | |  ||  || |||  || |  | ||| ||  | |||||| | ||||||||||| ||||| ||||||||||| || || || || ||| | ||||||||||| ||||||||||| || ||   ||||
ttagagatttgccaggtaagctata-ttacagaa-gaacatgtttaatgagcatgtctgttgcaagtgagaatagctgaggcaaggggaaagggttg--tgcagTCTTCGCACATCGTTGTGCCTGCAATTCAAGCCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAGTTTTTGAAAGTGAATCTGCCCAAAGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S119_132V6.1 (Physcomitrella patens), 3'ss of exon 4
--------gtatgatttggttg--caatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggcttt-cagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
        |  |     |||    | |||| |  |||    |      || ||  | |    |  |  |||         | ||      || | | ||| ||  | || ||||| || ||||||||||| || ||||||||||| || || || || ||| | |||||||||||| | |||||||| || ||   ||||
tccatagagatttgccaggtaagcctatttttcagaagaacatgtgtaatgtacatgtctgttgcaagtgaatggctgaggcaaggggagggttgtgcagCCTTCGCACCTCGCTATGTCTGCAATTTAAACCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAGTTCCTTAAAGTGAACCTCCCCAAAGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ37217 (Selaginella moellendorffii), 3'ss of exon 4
------------------gtatga--tttggttgcaatt----tgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
                  ||| ||  ||  ||  | | |    |||| || |     ||| | || ||   |   ||  |  ||   |   |   |   || | |   | ||||||  | ||||||||||||||||| || |||||||| || || || || |||||||||||||| ||||| |||||  | || |||||||| ||    |||
gtaagctctcgcacaccagtaggaacttcagtctcgactggagtgttggagtccg--tgttgtttcatcactttgatg-agatgggaatgaagcagtggaagg-gatgtgcagGCTACGCACATCGCTCTGCCTGCAGTTCAAGCCACACCACATCGCCGCCGGTGCCATTTTCCTGGCTGCAAAGTTTCTTAAGGTGAAGCTGCCGATCGAT

upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ27727 (Selaginella moellendorffii), 3'ss of exon 4
------------------gtatga--tttggttgcaatt----tgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
                  ||| ||  ||  ||  | | |    |||| || |     ||| | || ||   |   ||  |  ||   |   |   |   || | |   | ||||||  | ||||||||||||||||| || ||||| || || || || || |||||||||||||| ||||| |||||  | || |||||||| ||    |||
gtaagctctcgcacaccagtaggaacttcagtctcgactggagtgttggagtccg--tgttgtttcatcactttgatg-agatgggaatgaagcagtggaagg-gatgtgcagGCTACGCACATCGCTCTGCCTGCAGTTCAAGCCGCACCACATCGCCGCTGGTGCCATTTTCCTGGCTGCAAAGTTTCTTAAGGTGAAGCTGCCGATCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
                     atttgat  putative branch site (score: 5)
                                                ctttc  putative PPT
     tttatttttaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC