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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcgtaactaactcaccatccgttaccctagatctgcatataatttccccagatccgaacctcgctaaccctaatctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA

Basic information

species Glycine max
transcript GLYMA20G33270.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 1
gtaactcgtaactaa-ctcaccatccgttacccta----gatctgcatataatttccccaga--tccgaacctcgctaaccctaatctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA
   ||| ||  |    |  |     || |   |||    |||  | ||      |      |  || ||||    ||||   |  | | ||       |||||||| |||||||| || ||||||||||| ||||||   ||||||||||||||||| || | ||| ||||| ||||| || ||||||||||| ||||||||
catactggtgtccggtcgtattgctcggtggactaatatgattgggatgcggaatggttgaacttctgaactattctaagatttctgtgatgca--ttgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCACGGGCACCTTGACTATATTCGCACCGTGCAATTCCACCA

upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
--------------gtaactcgtaactaactcaccatccgttaccctagatctgcatataatttccccagatccgaacctcgctaaccctaatctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA
              |||  ||     || ||      |   |||    |||  | ||||    |      |||  |   ||  |||   |  | | ||       |||||||| |||||||| || ||||||||||| ||||||   ||||||||||||||||| || |  || ||||| |||||||| ||||||||||| ||||||||
tgttccgcctggttgtatttctgggatagct-gtgggctaatac----gattgggatatggaattgttgaatcgtagattc--taagatttctgtgatgca--ttgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA

upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g50350.1 (Oryza sativa), 3'ss of exon 1
gtaactcgtaactaactcaccatccgttac--cctagatctg-catataatttccccagat-----ccgaacctcgctaaccctaatctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA
 |   | ||    |   ||    ||  ||     | || ||| |||| |||     |  |      | ||||    ||||   |    | ||       |||||||| |||||||| || ||||| ||||| ||||||   ||||| |||||||||||||| |  |||||||| |||||||| ||||| ||||| ||||||||
-tgtattgttggcataacagtggcccatatgatttggaactgtcataaaataagatcgaacaactcctgaactcttctaagttttccgtgatgca--ttgcagGTGATGATTACAAGATTAAGGTATGGAATTACAAGACACACCGTTGCCTCTTCACGCTTCATGGCCACCTTGACTACATTCGCACGGTGCAATTCCACCA

upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 1
lower sequence: AC155622.2_FGT004 (Zea mays), 3'ss of exon 1
gtaact-cgtaactaactcaccatccgttaccctagatct--gcatataatttccccagatccgaacctcgctaaccctaatctaatctcaccc---gcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA
 || || | |   || |       |  |     ||||  |   ||| | |          | |  | ||    |   |  |  || | | |      ||||||||||||||||| || ||||| ||||| ||||||   || |||||||| ||||| || |  || |||||||||||||| ||||| ||||| ||||||||
-tagcttcctgtttaccgtggtggcaatctagttagactttgacatttcacgattgagcttacagatcttctaagatcctagttactgtgatgtaatgcagGTGACGATTACAAGATTAAGGTCTGGAATTACAAGACTCAACGCTGCCTATTCACACTTCATGGGCACCTCGACTACATTCGCACTGTGCAATTCCACCA

upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G149406_T01 (Zea mays), 3'ss of exon 1
-----gtaact-cgtaactaactcaccatccgttaccctagatctgcatataatttccccagatccgaacctcgcta-accctaatctaatctcacc-cgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA
      ||     | ||||||  || | | ||  ||  || |  ||    || |||    |  |  ||| ||    | |  ||  |    | | |||  |||||||| ||||| || || ||||| ||||| ||||||   ||||||||||||||||| || |  || || || |||||||| ||||||||||| ||||| ||
aatccatactaatgcaactaatacatccttcggcacattacaattgt---tacttttaagatttatgaatcttctaagattctggtactgttttaccatgcagGTGATGATTATAAGATTAAGGTCTGGAATTACAAGACGCACCGCTGCCTCTTCACACTTCATGGGCATCTTGACTACATTCGCACCGTGCAATTCCATCA

upper sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32142 (Selaginella moellendorffii), 3'ss of exon 1
gtaa----ctcgtaactaactcaccatccgtt--accctagatctg--catataatttccccagatccgaacctcgctaaccctaatctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA
||||      | |   |  ||||||   || |  ||  |   |  |  |     |||||      | |     |||||      |   |    ||      |||||| || ||||| |||||||||||||||||||||       | ||||| |||||||| || |||||  | || |||||||| || || |||||||| ||
gtaagatttccttgctttcctcaccgatcgatcgacattttgttcgatcgaccgatttctttgctttcctgagtcgctgctgaaaggatcccttctttttaagGTGATGACTACAAGATCAAGGTGTGGAACTACAAGACGAGGAGATGCCTGTTCACGCTGCTGGGCCATTTGGATTACATCCGGACAGTCCAGTTCCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catataatttccccagatccgaacctcgctaaccctaatctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA
                                           tctcaccc  CT-rich tract
                                   taatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcgtaactaactcaccatccgttaccctagatctgcatataatttccccagatccgaacctcgctaaccctaatctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC