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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttgagcttaataaaatgctttttattttgacttgcgtatcaaaaactatatgattctcatacttggtttcctgttgactacactcgtatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAAGAAACTCCAAGATGGCGTCAGCTCCTATCTAAACTTGGGCTGTAGCCAT

Basic information

species Glycine max
transcript GLYMA03G33360.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33360.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G58080.1 (Arabidopsis thaliana), 3'ss of exon 10
-----------------------------------------------------------------------atatttgag-cttaataaaatgctttttattttgac-----ttgcgtatcaaa-aactatatgattctcatacttggtttcctgttgactacactcgta-----tgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAAGAAACTCCAAGATGGCGTCAGCTCCTATCTAAACTTGGGCTGTAGCCAT
                                                                       || ||| |  |||| | |    |||| || |||  |        |||  || | || | | || || || | |    |||    |||   |   || ||     |  |||||   ||||||||||| ||  |  | ||||| |||||||| ||||||||||| || |||||||||||| ||||||||||    || || ||| | ||     
gttagtaatccctgccatttctctcttagtaatccctgccatttttttctcaattatcttactcccacccgatctttaaaacttattgatcctctttctacttttgcaccaaccacgttccacataaatctgtgtttatcgttccctcttttggtttggtcattttcataaatgttattgcagGCCGGAGGCAGTGGGGTATTAGTTTCACCTTTGACCTACATTTTTGATGAGGATACTCCAAGATGGGGTCAGCTCCTGAGAAACCTCGGGATTTAAATGC

upper sequence: GLYMA03G33360.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0035g00760.t01 (Vitis vinifera), 3'ss of exon 10
-------atatttgagcttaataaaatgctttttattttgacttgc-gtatcaaaaactatatgattctcatacttggtttcctgttgactacactcgtatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAAGAAACTCCAAGATGGCGTCAGCTCCTATCTAAACTTGGGCTGTAG-CCAT
       |||||    |  | |  | | ||   | | |  | |||  | || || ||       ||| | |  |    | |    || | | ||  | |||  ||||||||||||||||||||||||| || || ||  |||| || || || ||||||||||| ||||| |||||| |||| || ||  |||||||||| ||   || 
cacacccatattcacaccca-tccagtcctgggtttctctatttgttggattaagaa------aatttttaaccaccctgtgaactttattgcatccatatt-tgcagATTGGAGGCAGTGGAGTTCTAATTTCTCCACTGACATACATCTTCGATGAAGAAACACCAAGGTGGCGTGAGCTTCTTTCAGAACTTGGGCTCTAAATCA-
















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|10256425|gb|BE824191.1|BE824191
EST:     TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
EST: gi|58017604|gb|CX704346.1|CX704346
EST:     TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
EST: gi|51334857|gb|CO978723.1|CO978723
EST:     TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
EST: gi|15664845|gb|BI702216.1|BI702216
EST:     CTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: CTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
EST: gi|193350144|gb|FK317806.1|FK317806
EST:     TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
EST: gi|11273980|gb|BF324358.1|BF324358
EST:     TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
EST: gi|22541142|gb|BU090985.1|BU090985
EST:     TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
EST: gi|213599345|gb|DB979957.1|DB979957
EST:     TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
EST: gi|58014287|gb|CX701029.1|CX701029
EST:     TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCG                         ATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA
genomic: TATGTGTGCCTCAGAAGGCACTATACAAGTCTATACAACAACTGAGAGCGgtgagtttct ... tatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaactatatgattctcatacttggtttcctgttgactacactcgtatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAAGAAACTCCAAGATGGCGTCAGCTCCTATCTAAACTTGGGCTGTAGCCAT
                              tgttgac  putative branch site (score: 3)
     tatatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttgagcttaataaaatgctttttattttgacttgcgtatcaaaaactatatgattctcatacttggtttcctgttgactacactcgtatgatgcagATTGGAGGCAGTGGAGTTCTTATATCACCCTTGACCTATATTTTTGATGAAGAAACTCCAAGATGGCGTCAGCTCCTATCTAAACTTGGGCTGTAGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - aataaaa
- - - - - - - - - -tgctttt
- - - - - - - - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - - - - - - -caaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacactc