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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattttattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG

Basic information

species Glycine max
transcript GLYMA16G01230.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 6
------------------------------atatttgtactgtctcccatgatagttgtacggtgtgttctataca--attgtgttggtaacttagcttggctcatcattttattttttctggcgg-------ctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG
                               | |||  | |     |  || ||| ||     | |  ||   |    ||| |    ||   | |   |    |||  | ||  ||   |    |         ||||||||||||||||| |||||||||||||| ||||| || || || || ||||| |||||||| ||| | ||||| |||
gtaagtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtattttaccagttgttcaagattatgcattttctttcttacccatatgtattttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
-----------------------------atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattttattttttctggcggctc---cagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG
                               ||||    ||||     ||| | ||   | | |||   |    | |||||  |   || |  | || ||  | | |   |||    |||   ||    |||||||||||| ||||||||||| ||||| || || || || || |||||||| |||||||| ||| | || || |||
gtaagcactgcctggctctcatctctcctccatttac-ttgtcattgttgacattttagcagagtggcttgc-tacttgtgcagt--acatgacatgtctatttacta-gtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
-----------------------------atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttg-gtaacttagcttggctcatcattttattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG
                               ||||    ||||     ||| | ||   | | |||   |    | |||||  |   |    |  |    | | || ||||  ||   |  |   | |||||||||||||||||||||||| ||||| || || || || || || ||||| |||||||| ||| | || || |||
gtaagcactgcctggctctcatctctcctccatttac-ttgtcattgttgacattttagcagagtggcttgc-tacttgtgcagtacatgacatgtctatttaccagtttagcttgg-taacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 6
atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattttattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG
   |  ||  | | | ||||  |     | |  ||| ||  | |       |||    | ||       ||| ||     |   || ||   |  |  || ||||| || ||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||| ||||||
--gtaagttttttataccatcctcagcattct-tgtattggaaatgg--aagtttaagatttgcagaaactcttc---cgacaattgctattgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 6
atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattttattttttctggcggctcca-gAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG
   |  || ||||  |         |  |      |    ||| | | |  ||||  ||   |   |  |  |   | | | | | |||      |  | | ||||| || ||||||||||| || || |||||||| || || || ||||| |||||||| ||||| |||||||||
--gtaagttctgttgcttgatcagctccttttaactaacttattctacttggttgtaaaacaaa--tatcataatctctgactgtgtctaatattttgaagGGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------------------atatttgt-actgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattt--tattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG
                                                                                    || | | ||| | |   |  | | ||          ||      | |||| |    |   || |        | ||||  ||| | |  |      |  || || || || || |||||||| ||||| ||||| || ||||| || ||||| |||||||| ||||||||||| |||
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 6
atatttgtactgtctcccatgatagttgtacggtgtgttctatacaa-ttgtgttggtaacttagcttggctcatcattttattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG
  || || |||  ||     ||   |  || | |    |  |   |  || |  |   |   | |        || |  |||| |||  ||  || |  |||||||| ||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| |||||||||
gaatgtggactcactagttagaccttattatgattaaatgaagctatcttttactttcattgtcggaaaatagatgacattatgtttg-tgctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|209725663|gb|BW663152.1|BW663152
EST:     GTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC                         AGATGCTAGGGTTATGTGGGATCAGA
genomic: GTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTCgtaagtttca ... gcggctccagAGATGCTAGGGTTATGTGGGATCAGA
EST: gi|26058275|gb|CA801189.1|CA801189
EST:     GTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC                         AGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGG
genomic: GTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTCgtaagtttca ... gcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtgttggtaacttagcttggctcatcattttattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG
        tggtaac  putative branch site (score: 2)
                         tcatcattttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattttattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG

- - - - - - tctccca
- - - - - - - - - - - - - - - -ggtgtgt
- - - - - - - - - - - - - - - - - - - - - - - - -gtgttgg