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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag

Basic information

species Glycine max
transcript GLYMA08G24000.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 5'ss of exon 3
-------------------------------------GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag
                                     || |||||| | || || || |||||||||||||||||||||||||||||||| || ||||||||     ||  |||    |||     |   ||| ||   || |    ||   || || |   || ||    ||||    || | |  |           
TGGCGGCCTTGATCAGCAGATTAAGGAGATCAAAGAGGTTATTGAGCTTCCCATTAAGCATCCTGAGCTGTTTGAAAGTCTTGGAATTGCCCAGCCAAAGgttagaacttgtttatcagtttgcattttgtttggta--tcaactgtcattattagtggaaaatattcacctttg----atttttgcag----------

upper sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 5'ss of exon 4
GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag
||||||||  | || ||||||||||| ||||| ||||| |||||||||||||| |||||||||||     ||  ||       |  |  ||||   |   |||   | || |      |    |  |   ||| |||  | |                    
GTCATTGAACTTCCTATCAAACATCCAGAGCTATTTGAGAGTCTTGGAATTGCCCAACCAAAGgtttgaacttcttaacaatatcatcttaaacgatcctatttt-taagtattagcagaaaatattaactctcttttttcag-------------------

upper sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 4
GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgta-gtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag
||||||||| | |||||||||||||| || |||||||| || ||||||||||| |||||||||||  || |    |||||  |    |  |||  |||   | |  |   | |         |  |  | || | | |  |  |                   
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaagacggatcttgtttgtttttcag------------------

upper sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 4
GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgt--agtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctg--tttgctgaatctcttgatcacatcacag
||||||||| | |||||||||||||| || || ||||| || ||||||||||| |||||||||||  | | |||   ||  || |||  |   |  ||   | ||  | |   |||  | | ||  ||    |  |   ||  | | | | |              
GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttctctcttgaggcttgaagaccatcttaaccttttgaactttacatgtaggtggagaagactgagatcttatttattttttcag-----------

upper sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag
||||||||| | |||||||| ||||||||  |||||||   |||||||||||| || |||||||||   |   || ||     |  | ||  || |||| ||      |      || |  ||    |  ||| | ||     | ||| |            
GTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAGgtacacttgaatcttaaaccttcttctccatattgtgatgatgctaagtggattagacgtaatctcatctctctgtc---tttctag------------

upper sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag
||||||||| | ||||| ||||| ||||| |||||||| ||||||||||| || |||||||||||||| | |  || | |  || |||||  |  ||    |  ||| |||        || || ||||   | |       || |||| || |||      
GTCATTGAGCTTCCAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagt-tttagttgtagtatt-ttgctggagcttaa-gtatcataagctt------ttattaatttgatttt------gatttctttataacag-----

upper sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctgattttggggttgttgc---taaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag
|| |||||| | |||||||| ||||||||  | |||||||||||||| || || |||||||||||| |  ||   ||||  |||    |   |  || || |   |   ||     ||||     ||| |||||    | ||  ||||    |||    | |  |
GTTATTGAGCTTCCAATCAAGCATCCTGAATTATTTGAAAGTCTTGGTATAGCTCAACCAAAGgtacttcctttatttgtagttacatcatgtgtatcttattcatgtctcgaaggacttacaccttg-tttttgaaatagcccaatcaaa-gatgcttttattg

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|16346043|gb|BI971638.1|BI971638
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|16281730|gb|BI944638.1|BI944638
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|254349061|gb|GR860333.1|GR860333
EST:     AATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: AATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAA-TTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|192327448|gb|FK019605.1|FK019605
EST:     AATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAG
genomic: AATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAA-Ggtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAG
EST: gi|120533815|gb|EH261948.1|EH261948
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|26047693|gb|CA784406.1|CA784406
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|7028501|gb|AW458284.1|AW458284
EST:     CAATCAAACATCCTGAGCTGTTTGACAGTCTTGGAATTGCACTACCAAAT                         GGTGTCCTGCTCTATGGGCCACCTGGTACATGTAAAACATTGTTGGCTATG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|254333837|gb|GR848755.1|GR848755
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|15661720|gb|BI699091.1|BI699091
EST:     CACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|254323845|gb|GR840378.1|GR840378
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|37994568|gb|CF806272.1|CF806272
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACAT
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACAT
EST: gi|16281214|gb|BI944372.1|BI944372
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|151411634|gb|EV281445.1|EV281445
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|254325633|gb|GR838514.1|GR838514
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|15662663|gb|BI700034.1|BI700034
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|16280447|gb|BI943967.1|BI943967
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|151412070|gb|EV281882.1|EV281882
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|16284142|gb|BI945928.1|BI945928
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|7686556|gb|AW757204.1|AW757204
EST:     CAATCAAACATCCTGAGCTGTTTGAGAGTCTTGGAATTGCACAACCAAAG                         GGTGTTCTGCTCTATGGGCCACCTGGTACAGGAAATACATTGTAGGCTATG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|18734930|gb|BM528466.1|BM528466
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|120531685|gb|EH259818.1|EH259818
EST:     CAATCAAACATCCTGAGCTGTTTGACAGTCTTGGAATTGCACAANCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAANACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGG
EST: gi|151394633|gb|EV264504.1|EV264504
EST:     AATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGT
genomic: AATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAA-Ggtagtgtctg ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag

- - - - - - - - - - - - - -  GCTGTT