Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttacttttacttttctctttttctgttcatacaattagtttatatcttcattgatcttgggactcatgcttaacatcaaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGACGAGAGGAAAGCCTTGCTTGAGAAATTAGAACAGCAAAAAATTCAGAATT

Basic information

species Glycine max
transcript GLYMA20G39400.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39400.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G024389_T02 (Zea mays), 3'ss of exon 3
gtatatttacttttacttttctctttttctgttcatacaattagtttatatcttcattgatcttgggactcatgcttaacatcaaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGACGAGAGGAAAGCCTTGCTTGAGAAATTAGAACAGCAAAAAATTCAGAATT
                        |   |  |   | | | |      |  ||   | || | ||  ||       |  || ||| |   |||||||| |||| ||||| |||||||||||||||||  |||| ||||  || || | ||| || | | |  ||||| | ||   ||||||    ||  | |
-----------------------gtaaacaatctctgccagtgacagcttcctgattcgaacctg--acctgacaatgtcaccaatc---agGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAGGAAAAGAAGGCTTGGATCCAGAAACTCGAGAGGCAAAAGGGGCAAGAGT

upper sequence: GLYMA20G39400.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0150g00130.t01 (Vitis vinifera), 3'ss of exon 4
gtatatttacttttacttttctctttttctgttcatacaattagttt-ata-tcttcattgatcttgggactcatgc---ttaacatcaaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGACGAGAGGAAAGCCTTGCTTGAGAAATTAGAACAGCAAAAAATTCAGAATT
   |||  | |   | |     ||  |  | |  ||  | | |  || ||  | || || |  | |   || |   |   |   | | |   ||||||||||||| || ||||| ||||| |||||||||||| | ||| | |  || || | ||  || ||| |||||||  | || || |||||| |  ||||  
--gtataaaatcccaatcaatgctggtagtctctatctagtaaccttcatggtatttatcggacatcacacactgacatctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC
















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|7686618|gb|AW757275.1|AW757275
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|17519150|gb|BM188192.1|BM188192
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAG
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAG
EST: gi|20813295|gb|BQ297773.1|BQ297773
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|20813455|gb|BQ297933.1|BQ297933
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGGTTTCATGTTC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTC
EST: gi|38191377|gb|CF920583.1|CF920583
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|22524975|gb|BU083786.1|BU083786
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|213600215|gb|DB979794.1|DB979794
EST:     ACCCAGCCCATCAAG                         GATGACATC-GTGGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGAAA
genomic: ACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGT-GACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGA
EST: gi|15285711|gb|BI469602.1|BI469602
EST:     GCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: GCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|5678047|gb|AI939177.1|AI939177
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|120534415|gb|EH262548.1|EH262548
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|38192112|gb|CF921318.1|CF921318
EST:     AGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: AGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|5819909|gb|AI988176.1|AI988176
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCT
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCT
EST: gi|209701326|gb|BW655921.1|BW655921
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
EST: gi|10253606|gb|BE821372.1|BE821372
EST:     TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAG                         GATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC
genomic: TGACTCTTTTTGTGATATTTGCTGGAAGGAAATTCACCCAGCCCATCAAGgtatatttac ... caaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattagtttatatcttcattgatcttgggactcatgcttaacatcaaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGACGAGAGGAAAGCCTTGCTTGAGAAATTAGAACAGCAAAAAATTCAGAATT
                                    gcttaac  putative branch site (score: 3)
       tttatatcttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttacttttacttttctctttttctgttcatacaattagtttatatcttcattgatcttgggactcatgcttaacatcaaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGACGAGAGGAAAGCCTTGCTTGAGAAATTAGAACAGCAAAAAATTCAGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA