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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCAATGGACAAAGCCATTCTCTTAATGGTTACAGGAAGAGTTGTTGGTATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatatctctatttttctgtccttagactacccaattcgcttgttaataccgcattaagttaccatcttgcttaactggtcaaccaaaaacttgtc...

Basic information

species Glycine max
transcript GLYMA20G28340.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28340.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv05s0020g03200.t01 (Vitis vinifera), 5'ss of exon 1
GAGTCAATGGACAAAGCCATTCTCTTAATGGTTACAGGAAGAGTTGTTGGTATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatatctctatttttctgtccttagactacccaattcgcttgttaataccgcatta-agttaccatcttgcttaactgg--tcaaccaaaaacttgtc---
 ||| |||||| |||||||||| ||   |||||| |||||||||||||||||||| ||||||||||||||| |||| |||||||||||||| |||||||||||  |  |||      | |   || |||   || || |||     ||   |    ||||  | ||| |   |   | |||||   |||  || |||   |||   
AAGTTAATGGAAAAAGCCATTCACTGGCTGGTTATAGGAAGAGTTGTTGGTATGAGGAAGAGATTGAAGAGAACTTGAGATGGTGCTTTGCGCTCAATAGgta--ttaatcctcgcatgttaatcttta---tatcccatttatgagtaggttttccatttcaattaacccttgtttcaactgagatcagtcacaaaaa-gtcaaa
















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|9565859|gb|BE475368.1|BE475368
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|298184543|gb|HO029756.1|HO029756
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|298187240|gb|HO034389.1|HO034389
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|15203776|gb|BI426544.1|BI426544
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|8283967|gb|BE021526.1|BE021526
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|18040061|gb|BM308355.1|BM308355
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|298181023|gb|HO022462.1|HO022462
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|192327192|gb|FK017729.1|FK017729
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|298188703|gb|HO035396.1|HO035396
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
EST: gi|298191561|gb|HO039040.1|HO039040
EST:     TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAG                         TATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC
genomic: TATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatat ... gcggttgcagTATATTGCATACAGGAGCTAGCCAGTACCAAGACATTGCATTGTTGGACAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCAATGGACAAAGCCATTCTCTTAATGGTTACAGGAAGAGTTGTTGGTATGAAGAAGAGATTGAAGAGGACTTAAGATGGTGCTTTGCTCTCAATAGgtacatatatctctatttttctgtccttagactacccaattcgcttgttaataccgcattaagttaccatcttgcttaactggtcaaccaaaaacttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG