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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG

Basic information

species Glycine max
transcript GLYMA20G16100.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacct-ttagcagctatggtctaattaaaggcaataataa-tgattaaatgtttggtggggttt-gttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                                                             |  || ||| |    |  |   || | |  |||    ||    | |   | | |||    | | || |   | |||| ||  ||  |    |||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||||||||||||||| || || || || |||||||| |||
---------------------------------------------------------------------------atatttctagcaac---tctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g36950.3 (Oryza sativa), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacct-ttagcagctatggtctaattaaaggcaataataa-tgattaaatgtttggtggggttt-gttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG----------------
                                                                             |  || ||| |    |  |   || | |  |||    ||    | |   | | |||    | | || |   | |||| ||  ||  |    |||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||||||||||||||| || || || || |||||||| |||                
---------------------------------------------------------------------------atatttctagcaac---tctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGGTACCATTGATCTTCA

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G860590_T01 (Zea mays), 3'ss of exon 2
------------gtatgtgtgcgtatattttcttttttttagtctgttgttg-catcactttaatttgatgaa---aatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
             |||   | | | || | |  | ||||  || | |  |   ||||| | | | | ||| |     |||| | || ||       |  |||      ||   |  ||  |  | | | | |   |||   | |||  ||||        |||   | |  || |  ||||       ||||||||||| || ||||||||||| || |||||| | ||||||||||||||||||||||| || || || || ||||||||||||
gtgaggtccaaactatacctac-tctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatc---tttatctttcaatcatgcttgtggttacta-aatataaaaaaagaagggggaaatttctcatcgtcta-tgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G860590_T02 (Zea mays), 3'ss of exon 2
-------gtatgtgtgcgtatattttcttttttttagtctgttgttg-catcactttaatttgatgaa---aatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
        |||   | | | || | |  | ||||  || | |  |   ||||| | | | | ||| |     |||| | || ||       |  |||      ||   |  ||  |  | | | | |   |||   | |||  ||||        |||   | |  || |  ||||       ||||||||||| || ||||||||||| || |||||| | ||||||||||||||||||||||| || || || || ||||||||||||
gtccaaactatacctac-tctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatc---tttatctttcaatcatgcttgtggttacta-aatataaaaaaagaagggggaaatttctcatcgtcta-tgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagct-atggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                        |||   | | ||  |      | | || |       ||| | | | || ||     |   | | |     |     |   ||  |  || ||||  | ||| | |   | | |      |  || |   ||||||      | | ||||||||||||||| ||||||||| | || ||||||||||| |||||||||||||||||||||||||| ||||| || ||||||||||||
-----------------------gtttgtatttctttctaagaatcataaactctgcagtaattcatgtattcttt----tggggttttctcaaaaatattagattcaatattcagcacttcatgttttggattatgc-----accattacctaatgttatacttg-tatgttcagGCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAG

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S6_446V6.1 (Physcomitrella patens), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                                                       |  |  |   ||    |    |||   ||| |  |   |  || | |  ||  |   ||    |    || |||   ||   |||       | || || | |||||||||| |||||||| ||||| || |||||||| |||||||| |||||||||||||  || |||||  | || ||||| |||
-----------------------------------------------------------------------tgatacatgacagagcagtagttaccgcatttgctacgcgcttcgaatgtaaag---aagatgaaattatgata-caatctcatgagaaacagtgtctgattagGCTGCAAGCTTTGGAGGCTCCAACATAGATCCAACAGCTTGGGAAGACAAGAAGTGCCGCGGAGAATCAAGATTTCCTGCACAG

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                                                                                    |   | ||||  |||   |||    |    ||     |  | | | |   ||||   |   |        | |||||  ||||||||||||| ||||| || ||| |||| || |||||||||||||||||||  || || ||  | ||||| ||||||
---------------------------------------------------------------------------------------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaact--ctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                                                                            | | || | |||| |  |    || |  | ||     | | | |   ||    | |   |||  ||||   | |  | | |||||||| |||||||| || || || || ||||| || || ||||| ||||||||||| | ||| |||||||| |||||||| |||
-------------------------------------------------------------------------------------------gtaaagctacctctctcgc----aggatttgtgac---actcatgttgatggcga-gtccaaacttttgc--gtgactctacagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ18285 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                                                                            | | || | |||| |     | || |  | ||       | | |   ||    |  ||  ||  ||| | | |  |  | |||||||| |||||||| || || || || ||||| || || ||||| ||||||||||| | ||| |||||||| |||||||| |||
-------------------------------------------------------------------------------------------gtaaagctacctctctc----tcaggatttgtgactc---tcatgttgatggcga--atccaaacttttgcgtgactc-tacagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG

upper sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
                                                                                                    |   | ||||  |||    ||    |    ||     |  |   | |   ||||   |   |        | |||||  ||||||||||||| ||||| || ||| |||| || |||||||||||||||||||  || || ||  | ||||| ||||||
---------------------------------------------------------------------------------------------------gtacgtattacacttaagttcttctttgccgttgtcctctttggaact--ctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG

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|192309118|gb|FG999065.1|FG999065
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|14205657|gb|BG839335.1|BG839335
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|192313456|gb|FK005522.1|FK005522
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|58019242|gb|CX705984.1|CX705984
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|58018944|gb|CX705686.1|CX705686
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|11274562|gb|BF324905.1|BF324905
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|21602164|gb|BQ612495.1|BQ612495
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|192313455|gb|FK005521.1|FK005521
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|23735151|gb|BU765842.1|BU765842
EST:     ATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: ATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
EST: gi|254346210|gb|GR859823.1|GR859823
EST:     CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAG                         GCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG
genomic: CCATTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtatgtgtgc ... gtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG
    gtctaat  putative branch site (score: 3)
                                              tttgttc  putative PPT
       taattaaaggcaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT