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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTGTGTTTCCTGTGCTATCCATTCTCATGTTGTGAGGGTTCGATCCCGCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacactttttatagccatctctttatagccaaatggagatgatatagagagtgacatttatttactcaaaagtttagtaatggaagaatgtagagaat...

Basic information

species Glycine max
transcript GLYMA05G21370.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G56340.1 (Arabidopsis thaliana), 5'ss of exon 4
GTACTGTGTTTCCTGTGCTATCCATTCTCATGTTGTGAGGGTTCGATCCCGCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacactttt-tatagccatctctttatagccaaatggagatgatatagagagtgacatttatttactcaaaagtttagtaatggaagaatgtagagaat--
||||||||| || ||||||||||||||||| |||||||| || |||||||||||  |  | ||    |||   || ||||  || ||   ||| |||| ||||||   |   || |   |   | ||   | |     |  |   |    | |      ||   | |   ||    || ||         ||    |   |  
GTACTGTGTCTCGTGTGCTATCCATTCTCACGTTGTGAGAGTCCGATCCCGCACCAACCGTAGAGTTCGTACCCCACCACCTCGTTTTGCCAGACGCAAGgtaacctctcagtacaatgaatccattcgtgtccttcagcaaatttgcttaaatcagtcttagataa---aaggtcttggtggcattttgataataatggttt

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G40510.1 (Arabidopsis thaliana), 5'ss of exon 4
GTACTGTGTTTCCTGTGCTATCCATTCTCATGTTGTGAGGGTTCGATCCCGCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacactttttatagccatctctttatagccaaatggagatgatatagagagtgacatttatttactcaaaagtttagtaatggaagaatgtagagaat---------
 |||||||| |||||||||||||| |||||||| || || || || ||||||||  |  | |||   |||   |||||||  || |||  ||| |||| ||||| |  | |     |  ||| |||  |  |||     ||| ||  | ||  | |   ||  || |||||   |||  || |         |  |   |         
ATACTGTGTCTCCTGTGCTATCCACTCTCATGTCGTTAGAGTCCGTTCCCGCACCAACCGCAGGGTTCGTACTCCTCCACCTCGTTTCGCCAGACGCAAGgtaatatctct-----ctctctttttcgactcaat----gatcattaatagttttaagcttcatttctcaatcttttgttacttctgctcgctccattttgtctttggt

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 5'ss of exon 4
---GTACTGTGTTTCCTGTGCTATCCATTCTCATGTTGTGAGGGTTCGATCCCGCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacactttttatagccatctctt--tatagcca--aatggagatgatat-agagagtgacatttatttactcaaaagtttagtaatggaagaatgtagagaat
   |||||||||||| ||||| || ||||| |||||||| |||||||| ||||||||||| || ||||||||||| || || | ||| ||    || ||| |||||   || ||| |     ||| ||  ||| |  |  | |     || ||| |    |  |  ||| | |  | ||    |   ||| ||  ||     |     
GCAGTACTGTGTTTCTTGTGCAATTCATTCGCATGTTGTTAGGGTTCGTTCCCGCACTGACAGAAGGAAGCGTGATCCACCTCTGCGCTT---TAGACGCCGGgtatgtctatttttctttttcttttattattgttattattattattgttattattttgctatttttttctgtttaattactcgttaacggttgagaaatg-----

upper sequence: GLYMA05G21370.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv13s0067g02700.t01 (Vitis vinifera), 5'ss of exon 5
---GTACTGTGTTTCCTGTGCTATCCATTCTCATGTTGTGAGGGTTCGATCCCGCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacactttttatagccatctctttata-gccaaatggagatgatatagagagtgacatttatttactcaaaagtttagtaatggaagaatgtagagaat
   ||||||||| || ||||| || || || ||||||||||||||||| || ||||||||||||||||||||||| || |||||||| ||   ||| ||| |||||    || || |    || | | |||  |  | || |   ||||       |  |  |  |  | ||  || ||| || | ||     ||||    |  
GCAGTACTGTGTGTCTTGTGCAATTCACTCCCATGTTGTGAGGGTTCGTTCTCGCACTGATAGGAGGAAGCGTGACCCACCACAGCGCTT---CAGACGCCGGgtatgcgttattctgcttatttgtgtatttggtagattgttttgattgttgcggcaatctggaaat-ctagaatgttcagcattgtttttatgtgtgtaga

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|6070885|gb|AW100272.1|AW100272
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|192326591|gb|FK018838.1|FK018838
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGCCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|298198055|gb|HO039594.1|HO039594
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|26058129|gb|CA801043.1|CA801043
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCATG                         TATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|9205491|gb|BE331715.1|BE331715
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|31465608|gb|CD407636.1|CD407636
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACCAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|10238902|gb|BE807798.1|BE807798
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|151411510|gb|EV281321.1|EV281321
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|298192759|gb|HO033193.1|HO033193
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|31466786|gb|CD408814.1|CD408814
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|298183541|gb|HO028754.1|HO028754
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|298182602|gb|HO031337.1|HO031337
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|193542125|gb|FK496223.1|FK496223
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|298162975|gb|HO011708.1|HO011708
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|17023090|gb|BM094124.1|BM094124
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|192296480|gb|FG992316.1|FG992316
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|298197741|gb|HO045220.1|HO045220
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|4405733|gb|AI507882.1|AI507882
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|298163646|gb|HO012379.1|HO012379
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACGGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
EST: gi|21601683|gb|BQ612014.1|BQ612014
EST:     GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGG                         GATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC
genomic: GCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacacttt ... tcgttgccagGATGATGCACAAAGGCCTGGTCAGCCTGGTCAAGCTCCTCGTCCTGCTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTGTGTTTCCTGTGCTATCCATTCTCATGTTGTGAGGGTTCGATCCCGCACTGATAGGAGGAAGCGTGAGCCTCCACAGCGATTCATCAGGCGCAGGgtaacactttttatagccatctctttatagccaaatggagatgatatagagagtgacatttatttactcaaaagtttagtaatggaagaatgtagagaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatctct