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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA

Basic information

species Glycine max
transcript GLYMA08G34030.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 7
gttagagtgtcccctcaataaatgggctttgttgttctttggg----aattaaggacatg-ttagtctcaccttggcagtttttta-attgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
||| |  |    |  ||||      | ||||||  |   |  |    | || |   |||| |||   | |   | ||| | | ||| ||   |||| || || ||||||||| |  | || |||||  | |||||||||||||||||||| ||||||||||||||  | ||||| |||||  | ||  ||||||
gttggcat---tctccaatgcgcttgttttgtttatacataaggttaactttacatcatgattaacttgatggttgcattatattatatgacagGTGGACGAGAATTTTCTTATGAGGACATTTGGTCGTTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTCGAACAGAAGAGGAACGCAGAAGGCAAA

upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
              |   |   |  ||| ||  |||   |   | ||     | |  |  | | | |||  || |  | |  |  ||||| ||||| ||||||||| |  | || |||||  | |||||||||||||||||||| |||||||||||||| || ||||| |||||  | ||  ||||||
-------------gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttaca-tgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA

upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G133308_T02 (Zea mays), 3'ss of exon 7
gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
              |   |   |  ||| ||  |||   |   | ||     |||  |  | | | |||  || |  | |  |  ||||| ||||| ||||||||| |  | || |||||  | |||||||||||||||||||| |||||||||||||| || ||||| |||||  | ||  ||||||
-------------gttgctttctctgctgtgcggtttagttaaacttgtatgcattgtcttgttagctttaca-tgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA

upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
lower sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
--gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggcagttttttaatt--gtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
  |||      |  | |   |  ||    | |  | |||| | |  |||     | |  || ||  |   |   | |||| |  |   |||||||||||| ||||| ||||| || ||||| ||||||||||| || || |||||||| ||||||||||||||||| ||||| |||||||  ||||| ||||
gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggta-taattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA

upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
lower sequence: AT5G10800.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggc----agttttttaat----------tgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
||| |  | ||  |  | | ||    ||  |||||| |       |  |   |||  |  |||  ||||| |    | |||| |  |          | ||||||||||||||||||||||| || ||||||||||||||||| || || |||||||| || |||||||||||||| ||||||||||||| ||||||  |||
gtttgt-tctcatccaacttaaatacctgcgttgttttccatagctatatatcataattttcttcccttgcctaaaacttttgtggtattgtctttttttagGTTGATGAAAATTTTCTTCTGCGGACTTTTGGAAGATTTGGGCCAATAGCTAGTGTTAAAATTATGTGGCCAAGAACAGAGGAGGAGAAAAGGCGAGAAA

upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
                      | |  | | ||   |       |   ||||  || ||||||| |  | |   ||    | | | | ||      ||| ||  || ||||| ||||| ||||| ||| | |||||||||||||||||||| ||||| ||||||||||| || |||||||| |||||||| |||||  | ||||| ||||
gttgcattcctaatttttggatgctcaattctctgttattcttttactctttaatgctctttgg-acctgaaaccaacaaaatataatctgt---ttttattttttatagGTGGATGAGAATTTCCTTTTGCGTACTTTTGGAAGATTTGGTCCTATCGCTAGTGTGAAAATAATGTGGCCTAGGACAGAAGAGGAACGGAGGCGACAAA

upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S137_118V6.1 (Physcomitrella patens), 3'ss of exon 6
-------gttaga-gtgtcccctcaataaatgggctttgttgt----tctttgggaattaaggacatgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
       |||| |  | |      | ||  | || ||          ||        | | ||   |  || | |   |   |||  | |   | || |||||||||| || |||||  |  | ||||||||  ||||||| |||||||| ||||| || ||||||||||| |||||||| || ||| | ||||||||  
tcctctagttatacattttttggtagtagtttggtttaaggaaaatgtccacatctgtcacggttgtcgtacttttctcagagcatatatcgtaatgcagGTTGATGAGAACTTTCTGTTGAGAACTTTTGGGCGATTTGGGCCTATTGCCAGTGTAAAAATTATGTGGCCGAGGACAGATGAAGAGCGCAGGCGGCAGC

upper sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S196_109V6.1 (Physcomitrella patens), 3'ss of exon 6
--------gttagagtgtcccct--caataaatgggctttgttgttctttgggaatt-aaggac-atgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
          ||| ||||    |     |   |||     |   |  | || |  || || ||| || ||| | |      || || |  |    |  ||||||||||||| ||||||||  | ||||||||| ||||||| ||||| || ||||| || || ||||||||||||||||| || ||| | ||||||||  
tctcctcttgtagcgtgttgtttagtggtggttggtacagggactagtatgtgccttcaatgactatattactattctgaggggagctaatgtggttcagGTTGATGAAAACTTTCTTCTGAGAACTTTTGGACGATTTGGGCCTATCGCCAGTGTAAAAATCATGTGGCCAAGGACAGATGAAGAGCGCAGGCGGCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctttgggaattaaggacatgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA
                                           ttttaat  putative branch site (score: 3)
                                         tttttt  CT-rich tract
                                       agttttttaattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA