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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatctttaatgcatttctgatcttgtgtgtacttaccattttgatttgatgtttgttctggcattgaatgtaagtcattgcatttcttatctat...

Basic information

species Glycine max
transcript GLYMA09G38430.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 10
TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatctttaatgcatttctgatcttgtgtgtactta---ccattttgatttgatgtttgttctgg--cattgaatgtaagtcattgcatt-tcttatctat
||| || ||||| || |||||||||||||| ||||||||| | || ||||||| ||| |||||||||||| ||||||| || || ||   | |  ||    |     || |||  || |  ||   ||  |  | ||  ||||| |    ||  | ||  |||  |    | | ||| || ||     
TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttttcgaaattgtgct--attttgaatggagctaagtccggtggggttgcatgttagacaagggcctttttatgggaacagtaggattgtcctac----

upper sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 10
lower sequence: AT3G03340.1 (Arabidopsis thaliana), 5'ss of exon 10
TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatctttaatgcatttctgatcttgtgtgtacttaccattttgatttgatgtttgttctggcattgaatgtaagtcattgcatttcttatctat
||||||||||||||||||||||||||| || || |||||| |||| || ||||   | || || || ||| | || ||||  ||||   |     |     |   | ||||  ||  |   |   | |    | | || ||| |  |  | || | |  |                      
TGATCGCCGTTTAGCTGATCATTTTGGGGGGAAGCTTCATCTAGGATACATGCTAGTCCGGGACAAATTAACAGAGCTTCTGgtaaactaataacacaatctactttatctgatg-atggatgaaactgccttcttatatttctctt--cgtttacttcag---------------------

upper sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 5'ss of exon 10
TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatctttaatgcatttctgatcttgtgtgtacttaccattttgatttgatgtttgttctggcattgaatgtaagtcattgcatttcttatctat-
||| || || ||||| |||||||||||||| || |||||||| || |||||||| || ||||| ||| | || || ||||| ||||||    ||   | | |          | |   | |||   ||| | | |   ||  |||||    |   ||     | | | ||      ||   | 
TGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAGgtaagatgaattattttcgtgatcatataggagctcatttatgttttggttgtcccgtgggttctatt-tcatattggcattagtacaaaaaggataattt

upper sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S402_41V6.1 (Physcomitrella patens), 5'ss of exon 10
TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatctttaatgcatttctgatcttgtgtgtacttaccattttgatttgatgtttgttctggcattgaatgtaagtcattgcatttcttatctat---
||| || || || || || ||||||||||| || || ||||| || ||||||||||||||||||||| | |  ||  | |  ||| |   |  ||  | | || |     ||   |||  | |  |   || |     |  |||  || |    | ||  |   || | | |   ||  |     
TGACCGTCGCTTGGCGGACCATTTTGGAGGGAAGCTGCATTTGGGTTATATGCAGATTCGTGAGAAGCTCGTTGACTTGCGGgtacgcgcttatttctactttccaagattt---tgttttcaaaagcatggtaaagcgcgtgtattgcctggtagtgccacaaataggaatatctaagtggtgg

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|254336538|gb|GR842717.1|GR842717
EST:     AACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAA                         GAAGAAAGGAACAAGAGCCGAAAGACTGATCGGCTTGATGACAGGAG
genomic: AACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatc ... tctggctcagGAAGAAAGGAACAAGAGCCGAAAGACTGATCGGCTTGATGACAGGAG
EST: gi|254336539|gb|GR842718.1|GR842718
EST:     AACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAA                         GAAGAAAGGAACAAGAGCCGAAAGACTGATCGGCTTGATGACAGGAG
genomic: AACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatc ... tctggctcagGAAGAAAGGAACAAGAGCCGAAAGACTGATCGGCTTGATGACAGGAG
EST: gi|208146329|gb|GD946208.1|GD946208
EST:     AACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAA                         GAAGAAAGGAACGAGAGCCGAAAGACTGATCGGCTTGATGACAGGAG
genomic: AACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatc ... tctggctcagGAAGAAAGGAACAAGAGCCGAAAGACTGATCGGCTTGATGACAGGAG
EST: gi|16343424|gb|BI969019.1|BI969019
EST:     AACTTCANNNAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAA                         GAAGAAAGGAACAAGAGCCGAAAGACTGATCGGCTTGATGACAGGAG
genomic: AACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatc ... tctggctcagGAAGAAAGGAACAAGAGCCGAAAGACTGATCGGCTTGATGACAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAAgtaagacatctttaatgcatttctgatcttgtgtgtacttaccattttgatttgatgtttgttctggcattgaatgtaagtcattgcatttcttatctat

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT