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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag

Basic information

species Glycine max
transcript GLYMA07G00420.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 5'ss of exon 3
-------------------------------------GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctcattttggggtgttgctaaattttgtcattccatcagcag-cacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag
                                     || |||||||| || || || |||||||||||||||||||||||||||||||| || ||||||||     ||  |||    || ||||   |||||||  |   |||| | | ||   || || |   || ||    |||| |     | ||| |          
TGGCGGCCTTGATCAGCAGATTAAGGAGATCAAAGAGGTTATTGAGCTTCCCATTAAGCATCCTGAGCTGTTTGAAAGTCTTGGAATTGCCCAGCCAAAGgttagaacttgtttatcagt-ttgc---attttgtt-tggtatcaactgtcattattagtggaaaatattcacctttgat-----ttttgcag---------

upper sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 5'ss of exon 4
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgt----agtttctcattttggggtgttgctaaattttgtcatt--ccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag
|||||||| || || ||||||||||| ||||| ||||| |||||||||||||| |||||||||||    | ||  | |   |    | ||     ||  | |  ||    || ||||| | |  |      |  |||||| |                            
GTCATTGAACTTCCTATCAAACATCCAGAGCTATTTGAGAGTCTTGGAATTGCCCAACCAAAGgtttgaacttcttaacaatatcatcttaaacgatcctatttttaagtattagcagaaaatattaactctcttttttcag----------------------------

upper sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 4
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgt--agtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag
||||||||||| |||||||||||||| || |||||||| || ||||||||||| |||||||||||    |||||  |||   |    |  |||  |||   | |  |   | ||        |  |  | || ||   ||| | |                     
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaagacggatcttgtttgtttttcag---------------------

upper sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 4
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctg--tttgctgagtctcttgaacacatcacag
||||||||||| |||||||||||||| || || ||||| || ||||||||||| |||||||||||   || ||  | | | |  |||   |   |  | |     | | |   |||  | | ||   |    |  |   ||  | | | | |              
GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttctctcttgaggcttgaagaccatcttaaccttttgaactttacatgtaggtggagaagactgagatcttatttattttttcag-----------

upper sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctcattttggggtgttgctaaattttgtcattcc--atcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag
|||||||| || |||||||| ||||||||  |||||||   |||||||||||| || |||||||||   |   ||||    |  |  ||| ||| || |  | |  |   |      |  || ||| || |   ||| |||  | ||                   
GTCATTGAACTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAGgtacacttgaatttcaaagcttatctatattgtgacgctgctaagtggatttcgaactgattgcttctccctctcttt--taag-------------------

upper sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctcattttggggtgt-tgctaaattttgtcattccatcagcagcacacttggttgttt-atttttctgtttgctgagtctcttgaacacatcacag
||||||||||| |||||||| ||||||||  |||||||   |||||||||||| || |||||||||   |   || ||      | | ||  || |||| ||      |   | |      ||  | | || | ||||| |    ||                   
GTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAGgtacacttgaatcttaaaccttcttctccatattgtgatgatgctaagtggattagacgtaatctcatctctctgtctttctag-------------------

upper sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag
||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| || |||||||||||||||| |  || | |  | |||||  |  ||           || | || |    | | ||||||  | || ||      ||| |  ||||        
GTCATTGAGCTTCCAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgtagttt-tagttgtagtattttgctggagctta----------agtatcata---agct-tttattaatttgattttgatttctttataacag-------

upper sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag
|| |||||||| |||||||| ||||||||  | |||||||||||||| || || |||||||||||| || ||   ||||  ||      |  | |      | |||     | |    |      || |||||    | ||  | ||    ||     | |  |
GTTATTGAGCTTCCAATCAAGCATCCTGAATTATTTGAAAGTCTTGGTATAGCTCAACCAAAGgtacttcctttatttgtagttacatcatgtgtatcttattcatgtctcgaaggacttacaccttgtttttgaaatagcccaatcaaa-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|37996482|gb|CF808071.1|CF808071
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGNTACAGGTAAAACAT
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACAT
EST: gi|151403300|gb|EV273110.1|EV273110
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         G-TGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|37995024|gb|CF806613.1|CF806613
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|18732952|gb|BM527342.1|BM527342
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|15589715|gb|BI674331.1|BI674331
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|16281256|gb|BI944393.1|BI944393
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|16277739|gb|BI942538.1|BI942538
EST:     CAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|120534038|gb|EH262171.1|EH262171
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGT
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGT
EST: gi|18039807|gb|BM308101.1|BM308101
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|16281818|gb|BI944685.1|BI944685
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|37995944|gb|CF807533.1|CF807533
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|19052933|gb|BM731600.1|BM731600
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|193689693|gb|FK632268.1|FK632268
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
EST: gi|37995965|gb|CF807554.1|CF807554
EST:     CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG                         GGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG
genomic: CAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctc ... cacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgtagtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag

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