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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaacttggctgctgcaatgaaacacagcatattgaaaaatgtttcatgcattataagtttgtattagtgtcacagcttgacaaaattgatagcg...

Basic information

species Glycine max
transcript GLYMA09G31920.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G31920.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os03g50300.1 (Oryza sativa), 5'ss of exon 15
--TGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaacttggctgctgcaatgaaacacagcatattgaaaaatgtttcatgcattataagtttgtattagtgtcacagcttgacaaaattgatagcg
  ||| |||||| ||||||||||||     |||||||| ||  | || |||||||| || ||||||||||| ||||||||||||||||| || ||||| ||||| ||  ||  |    | |  |    |||     ||||   |   |  |  ||   |||||  |   | ||| |  || | |  |               
TATGCAGAAGATGTTGAAAGTGGTTCT---TCAGATGTTGAGACGAAGTACAAGAAAATGTATGAGGATGACATAAATCCTTTTGCTGCTTTTTCAAAGAAGgtaacaaaatgtttacgttttatgataacgtgttatat---acgttactctatagcttatacatacat-ttaattccatatccag---------------

upper sequence: GLYMA09G31920.2 (Glycine max), 5'ss of exon 8
lower sequence: AT3G18480.1 (Arabidopsis thaliana), 5'ss of exon 16
TGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaacttggctgctgcaatgaaacacagcatattgaaaaatgtttcatgcattataagtttgtattagtgtcaca-gcttgacaaaattgatagcg
||  ||||||||||||||||| ||||  || ||||| ||||| ||||||||||| || || || ||||| || || |||||||| |||||||| |||||||| |   |       | |||| || |   |||  |   | | |  | |||| |  |   |||   | |  || |   |   | |||| |            
TGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAAAGgtaaaaaataaaacattctgctatcatcgacacaagccttatatttctttcctaaacattaaccctttcctatttatatgtgtttgatag-----------

upper sequence: GLYMA09G31920.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv17s0000g03970.t01 (Vitis vinifera), 5'ss of exon 16
TGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaacttgg-ctgctgcaatgaaacacagcatattgaaaaatgtttcatgcattataagtttgtattagtgtcacagcttg-acaaaattgatagcg--
| | ||||||||||| ||||||||||  |||||||| ||||| || |||||||||||||||||||||||||||||||| |||||||| ||||| ||||||||       ||||  || ||    ||||     ||| |||  | ||   || |||  | | || ||   | ||  |    |  ||| |   || | || ||   
TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatt--tgca-attttataacaatttatgtgtca-aacttgaaactaaagcatgattttggatttaaatcattgcttc

upper sequence: GLYMA09G31920.2 (Glycine max), 5'ss of exon 8
lower sequence: PP1S1_786V6.1 (Physcomitrella patens), 5'ss of exon 16
TGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaacttggc-tgctgcaatgaaacacagcatattgaaaaat--gtttcatgcattataagtttgt-attagtgtcacagcttgacaaaattgatagcg
 |  || ||| | |||   ||  |   |   ||||| ||    | |||||||||||| ||||| |||||||| ||||| ||| |||| || ||||| |||||   |   |||  |    |||   ||| || | | | |   |  ||  ||||  |  |    |  ||| | | |  | |    |  | |     || ||    
CGGGGAGGATTTGGAATCAGGAATGGGGGGTGATGTAGAGAGCAGATACAAGAAGATGTATGAAGATGATATTAATCCGTTTACTGCTTTTTCAAAGAAGgttgttattcttttcgcaatgcgcagaatcagaccgtctatcagcattggttttgtttacagcacatttcttactcctctttgcgtctcatttttttaat----

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|120496573|gb|EH224740.1|EH224740
EST:     AGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAG                         GAAAGGGATCAAAGATACAAGGAGTTAGGATTCAGGGACAGAATTACACTC
genomic: AGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaac ... atgtaattagGAAAGGGATCAAAGATACAAGGAGTTAGGATTCAGGGACAGAATTACACTC
EST: gi|120494352|gb|EH222519.1|EH222519
EST:     AGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAG                         GAAAGGGATCAAAGATACAAGGAGTTAGGATTCAGGGACAGAATTACACTC
genomic: AGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaac ... atgtaattagGAAAGGGATCAAAGATACAAGGAGTTAGGATTCAGGGACAGAATTACACTC
EST: gi|9203341|gb|BE329627.1|BE329627
EST:     AGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAG                         GAAAGGGATCAAAGATACAAGGAGTTAGGATTCAGGGACAGAATTACACTC
genomic: AGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaac ... atgtaattagGAAAGGGATCAAAGATACAAGGAGTTAGGATTCAGGGACAGAATTACACTC
EST: gi|51338349|gb|CO982215.1|CO982215
EST:     AGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAG                         GAAAGGGATCAAAGATACAAGGAGTTAGGATTCAGGGACAGAATTACACTC
genomic: AGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaac ... atgtaattagGAAAGGGATCAAAGATACAAGGAGTTAGGATTCAGGGACAGAATTACACTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaacttggctgctgcaatgaaacacagcatattgaaaaatgtttcatgcattataagtttgtattagtgtcacagcttgacaaaattgatagcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC