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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacactgcaaagcattgttggttatatgatcatgcatgtcaaagtgtcttttgatctttgatttccattttaaaacag

Basic information

species Glycine max
transcript GLYMA12G03640.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G374574_T02 (Zea mays), 5'ss of exon 16
TTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacactgcaaagcattgttggttatatgatcat----gcatgtcaa-agtgtcttttgatctttgatttccatt-ttaaaacag
| | || ||    | |||| |   ||| |  || |||||||| ||||| |||||||||||||| || ||||| |||||||| || || || || || || ||| |             ||  |   || |   |||      |||    |  ||  ||  |||       || | ||| ||   ||||
TACTTCAAATTCAACTGGGGCAGTAGAGTCCGCTGATGATGATTTGCCTAGTGTGATGACGTGCGCCAATTATCTGAAGCTGCCCCCCTACTCCACAAAAgtacagtgtccttgctgttttatcactaaaaagtcagcttgacattctgatggttcctgctgacgggctgttgctattgtttggacag

upper sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 16
lower sequence: AT4G38600.2 (Arabidopsis thaliana), 5'ss of exon 16
TTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaaca---ctgcaaagcattgttggtt-atatgatcatgcatgtcaaagtgtcttttgatctttgatttccattttaaaacag
  || | |||||    ||| |||| ||   |||||||||||| ||||| ||||| ||||| || ||||| ||||| || || |||||||||||||| |||||    ||   || | |  | |  |  ||  || | |   ||  |||    | | ||   ||  | |   ||     || ||||||
AGCAGCCAACGGAGCAGGGGCTTCGGAGACAGCAGATGATGATTTGCCCAGTGTCATGACTTGCGCAAACTACCTTAAACTCCCTCCTTATTCTACAAAGgtgagtcatgtcttctattcttcttgagtccatgttagtgtggttgttggtgagcctgaggagttgtatgtta----ttgaaacag

upper sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 16
TTCATCTAACGGGAAT---GGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacactgcaaagcattgttg-gttatatgatcatgcatgtcaaagtgtcttttgatctttgatttccattttaaaacag
   | | || || | |   || || || |||| ||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| || ||||||||||||    | |     | |||||   | | |      |  ||||     ||     || | | | |  |||| ||   || |||
---AGCCAATGGTAGTTCTGGCCCATCGGAATCAGCGGATGATGACTTGCCCAGTGTCATGACATGTGCTAATTACCTCAAGCTTCCTCCGTACTCTACCAAGgtatggtatttttgtgaattgtgaagatgtccaggaactcatggatttgttgtcattaaccatcgccttccttt---aaccag

upper sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 5'ss of exon 16
TTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacactgcaaagcattgttggttatatgatcatgcatgtcaaag---tgtcttt-tgatctttgatttccattttaaaacag--------------------
  || | |||  || ||| ||||| |||| ||| || || || ||||| ||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||||||| || | |  ||   || || | |    |||  ||  |  ||| |    |  ||   || ||    ||   |  ||||||                        
GGCAACCAACATGATTGGACCTTCTGAATCAGCCGACGAGGATTTGCCCAGTGTTATGACTTGTGCCAATTACCTCAAGCTTCCTCCCTATTCCACCAAGgtaaaaaaat-taatatatggtagatatgttgaaaataaaaatcagatacctaactgcatgctcacacatgctctatttaaatttacctttcccctttcctttcag

upper sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 16
lower sequence: PP1S116_90V6.1 (Physcomitrella patens), 5'ss of exon 11
TTCATCT--AACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgt-agaacact-gcaaa-gcattgttggttatatgatcatgcatgtcaaa-gtgtcttttgatctt--tgatttccattttaaaacag---------------------------------------------------------------------------
|  | ||  | | ||||||||    |    || || ||    ||  |||| ||||||||||||||||| || || |||||||||||||| || ||   |||||| || |   | |   | ||     | | |   || |   | |  |     |||  | |  | | |  ||| | ||   |  | |                                                                              
TGGAGCTGCAGCAGGAATGGGG--ACGACGTTGGCGGACAGGGATCTGCCGAGTGTGATGACGTGTGCGAACTATCTGAAGCTTCCTCCGTACTCATGCAAGgtgaggatgtttgtggacgcgggacttggtgcgtggttgcgtactttgggtgtgcatgtgtagcgtagtgagtaccgagtggagatgcagagatttggttgcggcgggcttcttgggatggttagtagagttggtactgacagggtggtgagtgtatgtgcag

upper sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 16
lower sequence: PP1S263_1V6.1 (Physcomitrella patens), 5'ss of exon 9
--TTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacactgcaaagcattgttggttatatgatcatgc-atgtcaaagtgt---cttttgatct--ttgatttccattttaaaacag----------------------------------------------------------------------
        || | ||  ||||    |    || || ||  | ||| |||| ||||||||||| |||||||| ||||||||||||||||| || ||   ||||||       | |   |      | | |    | |       | |    |||    | | |   ||  ||  ||     |  | |  |                                                                       
GGGAGCCTTAGCAGGGTTGGGG--ACCACGTTGGCGGACAAAGACCTGCCCAGTGTGATGACATGTGCAAACTACCTGAAGCTTCCTCCGTACTCGTGCAAGgttaggatgttcgtggtggaagttggtgcggggttgcattgtttgggggtgcacgcgtgtagcctagttagttatgggtggagatgaatcgatttagttgtgacgtgttggcatggtgagtaaagttggtactgaatgggtgtgggtgatgttcacag

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|8286288|gb|BE023847.1|BE023847
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|9259017|gb|BE347164.1|BE347164
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTNCTTCTTATTCTACCCAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGAATC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGA-TC
EST: gi|193345012|gb|FK311638.1|FK311638
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|193626370|gb|FK577046.1|FK577046
EST:     TGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: TGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|21602284|gb|BQ612615.1|BQ612615
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|192314633|gb|FK008141.1|FK008141
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|193406557|gb|FK375516.1|FK375516
EST:     AAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGGATC
genomic: AAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCA-GGGATC
EST: gi|193691482|gb|FK630201.1|FK630201
EST:     GTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|51335365|gb|CO979231.1|CO979231
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|12688675|gb|BG155011.1|BG155011
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|254331304|gb|GR845883.1|GR845883
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
EST: gi|192314634|gb|FK008142.1|FK008142
EST:     GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAG                         GAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC
genomic: GTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacact ... tttaaaacagGAAATTATGTACAAGAAGCTACTCTATGCAATCAGTGAAGGCCAGGGATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCATCTAACGGGAATGGGCCTTCAGAATTAGCAGATGATGACTTGCCAAGTGTGATGACGTGTGCAAATTACCTGAAGCTTCCTCCTTATTCTACCAAGgtagaacactgcaaagcattgttggttatatgatcatgcatgtcaaagtgtcttttgatctttgatttccattttaaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC