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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaatctattctttgcattgctgttctttaagcatgataatcttttttttttcttgcttttatttactccttttatgttgtttgaatag

Basic information

species Glycine max
transcript GLYMA19G01260.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01260.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os08g29370.1 (Oryza sativa), 5'ss of exon 6
GAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaatctattctttgcattgctgttctttaagcatgataatcttttttttttcttgcttttatttactccttttatgttgtttgaatag--------
|| ||||| |  ||||||||||||||||||||||| |||||||| || || |||||||||||||| |||||||| || |  ||        | || ||   |   | ||||||    |  | |     | |||      |||| ||    |||    |||||||||         
GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgctt--cagcattttctaacattaaac-gtttgaatatcatggcag

upper sequence: GLYMA19G01260.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G015967_T01 (Zea mays), 5'ss of exon 6
GAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaatctattct-ttgcattgctgttctttaagcatgataatcttttttttttcttgcttttatttactccttttatgttgtttgaatag---
|| |||||||  ||||||||||||||||| || || || || ||||| || |||||||| ||||||||||| || ||    |  |      |||||    |   | | | ||| ||  ||||   |  | |||    | |  | ||      ||  ||   || ||     
GAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAAgtaagagagacatgcaagattgcacatatcagcat-atgca-gacgatctgcatcgtatctaatgtattctaacctgagataacttcactgcatgacag

upper sequence: GLYMA19G01260.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv14s0066g01410.t01 (Vitis vinifera), 5'ss of exon 6
GAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaatctattctttgcattgctgttctttaagcatgataatcttttttttttcttgcttttatttactccttttatgttgtttgaatag---------
||||||||||| ||||||||||||||||||||||| |||||||| || || |||||||| |||||||||||||| || |   |  |||| |  ||| ||| || | ||   |||   ||    ||  |  ||   |  |||||  || |||| |||| ||| | |           
GAGCTTGGTCTGTACAAGGCTCAAACAAAGCTTCCATTTAATGCATTTGGAACAATGGCCATGGCAAGAGATgtaagaactcta-attcataccatggctatt-tctacatatgtgtatggacttgatggctaaatgatatttgttctttttttgttttttcattttactctgcag

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|15589721|gb|BI674337.1|BI674337
EST:     AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|209701975|gb|BW661361.1|BW661361
EST:     AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|13480110|gb|BG509453.1|BG509453
EST:     AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|31474078|gb|CD416106.1|CD416106
EST:     AAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|31463367|gb|CD405395.1|CD405395
EST:     AAACTAAGCTTCCGTTTAATGCTTTCGGTACCATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|20208026|gb|BQ134115.1|BQ134115
EST:     AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|27424039|gb|CA935559.1|CA935559
EST:     AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|31309102|gb|CD394305.1|CD394305
EST:     TGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: TGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|213596546|gb|DB974022.1|DB974022
EST:     AAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAA-TTGAAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGA
genomic: AAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTG-AGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGA
EST: gi|209726777|gb|BW672491.1|BW672491
EST:     AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA
EST: gi|20812710|gb|BQ297188.1|BQ297188
EST:     AAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT                         GAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAA
genomic: AAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaa ... gtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGATgtgaggagaatctattctttgcattgctgttctttaagcatgataatcttttttttttcttgcttttatttactccttttatgttgtttgaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA