Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcttgatgcattctgaatctctggtttttactgttttgttgattagtgtctgacttaccaatgtcctactgaccagttactccttttgcattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCACCCATACTCTATAATAGAGTGTGAGCCTAAGCGTGAA

Basic information

species Glycine max
transcript GLYMA18G47780.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------gttcttgatgcattctgaatctctggtttttactgttttgttgattagtgtctgacttaccaatgtcctactgaccagttact---ccttttgcattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCACCCATACTCTATAATAGAGTGTGAGCCTAAGCGTGAA-
                                    |  |  ||| |    | | | || ||| |  |     |  | ||  ||| |  |||  |  |     | | |  | ||  |    || ||  ||||  | |||||| ||||| ||| || ||||| ||| ||||  |    ||  ||||||| ||||| |||||||| ||||||||||| || ||||| || ||||||||| 
gtaaattctccatatatcaatactgtctcagctatcttctattgcctgtgtattttttgttttcttgtagcaaggggctttttgttttgcttgtctttccgagatttaataattgatggatctcttttattatataagGTTGTTTTCATTGGAGGACGTACTCAAACTGGTTCAGTGAAATCTGATGAAGGGGAACGCCACCCTTACTCTATAATCGACTGTGAACCAAAGCGTGAAG

upper sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 5
--gttcttgatgcattctgaatctctggtttttactgttttgttgattagtgtctgacttacca-atgtcct-actgaccagttactccttttgcattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCACCCATACTCTATAATAGAGTGTGAGCCTAAGCGTGAA-
  | | |||    |||||  || | |  |||    |  |||| || | |   |   | |||  | ||    | | |    | ||| |  ||||  |||||| |||||||  ||||| || ||||| ||||||||||| || || ||| ||||||||||||| ||||| || ||||||||||| || ||||| ||||| |||| | 
tgggttttgtacaattct--atttttattttcctgtcatttgctggtgaa-ataacatttattatatactttgatttgggatttaattatttt--attactgcagGTTGTCTTCACCGGAGGTCGCACACAACCTGGCACAACAAAGTCTGATGAGGGGGAGCGCCATCCTTACTCTATAATTGATTGTGAACCTAATCGTGTAG
















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|120531863|gb|EH259996.1|EH259996
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|23727845|gb|BU761958.1|BU761958
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|9902134|gb|BE611102.1|BE611102
EST:     CTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: CTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|21889224|gb|BQ742437.1|BQ742437
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|10233547|gb|BE802435.1|BE802435
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|10709161|gb|BF008885.1|BF008885
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|17963939|gb|BM270682.1|BM270682
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|4292136|gb|AI437719.1|AI437719
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGNGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|14126644|gb|BG791082.1|BG791082
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|24135721|gb|BU926231.1|BU926231
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|23730459|gb|BU763318.1|BU763318
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|14125668|gb|BG790106.1|BG790106
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|17518498|gb|BM187540.1|BM187540
EST:     TTTTTATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|19345855|gb|BM890735.1|BM890735
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|20811794|gb|BQ296272.1|BQ296272
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|151410055|gb|EV279863.1|EV279863
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|18039719|gb|BM308013.1|BM308013
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|11275114|gb|BF325437.1|BF325437
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGTAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|18041364|gb|BM309658.1|BM309658
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|151394651|gb|EV264522.1|EV264522
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|120494210|gb|EH222377.1|EH222377
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|11413000|gb|BF425020.1|BF425020
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|18041470|gb|BM309764.1|BM309764
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|7795709|gb|AW781106.1|AW781106
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|209702200|gb|BW673232.1|BW673232
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|9987802|gb|BE661910.1|BE661910
EST:     ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: ATTGAATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
EST: gi|16345992|gb|BI971578.1|BI971578
EST:     AATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGA                         GGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA
genomic: AATCTTCAGACCTTAACTTTTCAAGATACGGTGACACCTTTTTTGAggcaagcttc ... cattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtctgacttaccaatgtcctactgaccagttactccttttgcattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCACCCATACTCTATAATAGAGTGTGAGCCTAAGCGTGAA
                       tactgac  putative branch site (score: 1)
                                    ctccttttgc  putative PPT
                                              attactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttgatgcattctgaatctctggtttttactgttttgttgattagtgtctgacttaccaatgtcctactgaccagttactccttttgcattacttcaGGTTGCTTTCACTGGGGGTCGTACACAACCTGGAACTACCAAGCCTGATGAGGGGGACCGCCACCCATACTCTATAATAGAGTGTGAGCCTAAGCGTGAA

gttcttg
- - - - -gcattct
- - - - - - - - - - -tctggtt
- - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - -gtgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgacca