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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag...

Basic information

species Glycine max
transcript GLYMA04G39490.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 5'ss of exon 3
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctc---tacataactg----catagtccaattagaat----ttagccataaaaga-gtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag
 | ||  | || ||| ||||||||||||| ||||||  ||||||  ||||| |||| |||||||||||||| |||||  ||||  |||| || || |||||||| ||    |||| || |     |||    || | | | |    | ||||| |   ||    |||   |   |  | || |||| | | |  ||||              
TCAACCATCTTTTGGGTTGGAGAATGGTTTATAAAGAAAATGCCATTTGTTCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgtatacttccatacacaaatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcag--------------

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 4
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcata---gtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag-
 | ||||| || ||||||||||||||||| || |||  ||||||  |||| ||||| ||||| |||||||| |||||  | ||  ||||  | || ||||||      ||| ||  | || |    |    || ||| |   | |   | ||  ||  |  |    ||   |||||| |   | |   |  ||  |||  | | 
TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactc---attcatgtttttcacttg-gagtgacacattga

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G052855_T01 (Zea mays), 5'ss of exon 4
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag--------
 | || || |||||| ||||||||||||| ||||||  ||||||| |||| ||||| |||||||||||||| |||||  | ||  ||||  | || |||||||   | || || | | || |   | |||  |  |   ||| ||      ||||  ||   |  | | ||| |    ||      ||     | |||||        
TCAACGGTCTTCTGGGTTGGAGAATGGTTTATAAAGAAAATGCCCTTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGCACTGCTGTTTCACCAGgtaa--tgta-attagtacacaactccattctacgtgcaccagaatg----ttgaacgtccatatt-atttcttcaaaatttattttagctttcctgtagaggagtcc

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G073415_T01 (Zea mays), 5'ss of exon 4
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATAT-CTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag---
 | ||||| |||||| ||||||||||||| |||||   ||||||  |||| ||||| |||||||||||||| |||||  | ||| ||||  | | | |||||||      |  |   | ||||  |   |   | | ||     |  |  ||| |    |   |  | |  || |    |       ||     | |||||   
-CAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTTTCACCAGgta-atgtaattttttttcatacgcagctccaattctacgtgcaccaatgtt-gtccatccatatt-atctcttcaaaaaatattttagctttcctgtagagg

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G048150_T03 (Zea mays), 5'ss of exon 4
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag---
 | ||||| |||||| ||||||||||||| |||||   ||||||  |||| ||||| |||||||||||||| |||||  | ||| ||||  | || |||||||      |  |   | ||||  |   |   | | ||     |  |  ||| |    |   |  | |  || |    |       ||     | |||||   
TCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTTCACCAGgta-atgtaattttttttcatacgcagctccaattctacgtgcaccaatgtt-gtccatccatatt-atctcttcaaaaaatattttagctttcctgtagagg

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G073415_T03 (Zea mays), 5'ss of exon 4
-------GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag
        | ||||| |||||| ||||||||||||| |||||   ||||||  |||| ||||| |||||||||||||| |||||  | ||| ||||  | |                                                                                                          
GGTGGGTTCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt----------------------------------------------------------------------------------------------------------

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 5'ss of exon 4
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctaca-taactgcatagtccaatta---gaatttagccataaaagagtttgatg-gtgggttctgaattcatatggatgagcagtaagccacatgtag
||||||||||||||| ||||||||||||| |||||| |||||||| |||||| |||||||||||| || |||||||| || ||||| ||||| ||||||||||    ||  | |   |  | | |     |    || |||   |    |   ||||| ||      | ||    | ||    || |   | ||           
GCCACTGTTTTCTGGCTTGGAGAATGGTTTATAAAGAGAATGCCCTTTGTTAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctgaagtttttttacatttttgcttaccgactttcaacgcctagttgtttggtgcaaaaatacttgcattatgaacataaattgaaatttctg-----

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S126_74V6.1 (Physcomitrella patens), 5'ss of exon 4
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctac-ataactgcatagtc--caattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag
 |  ||||  |   | |||| ||||||||||| ||||| ||||| ||||| | |||  | |||||||| || ||||| || |||||||| || |||||||||||    ||   |   ||     ||  || ||||  |  | |  | |      |   | |    || ||| ||  |          |  ||||| ||     
ACATCTGTGATAACGGTTGGCGAATGGTTCATCAAGCGCATGCCACTTGTGAAGCAAGTTTACTCTGCTTCGAAGCAAATTAGTGCTGCCATTTCTCCAGgtatatcttattgttgttgtggcatcgacagttagt-tacaactgtgatgtttctacttcgcaaatt-tgagttagtgatagcagata-caagccccactcgt

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S51_161V6.2 (Physcomitrella patens), 5'ss of exon 5
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttg---atggtgg-gttctgaattcatatggatgag-cagtaagccacatgtag---
 |  ||||  |   | | || |||||||| || || || ||||| ||||| | |||  | || ||||| || |||||||||||||||||||| |||||||||||           || ||| || |  |   |  ||||  ||   ||| ||     | | ||| |||   || |||| | ||||   |   |||    |   |    
TCATCTGTGATAACGGTGGGCGAATGGTTTATTAAACGCATGCCTCTTGTGAAGCAAGTTTATTCTGCCTCGAAGCAGATCAGTGCTGCAATCTCTCCAGgtatagctc------cttcattgttc--tggaatcttagtgatggtagatttcagcaacgttggtgttgcaaactcatgtagatggttccacaagttgaaacgacttc

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S126_73V6.1 (Physcomitrella patens), 5'ss of exon 5
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatg--ctctacataactgcatagtccaat----tagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag
 |  ||||  |   | |||| ||||||||||| ||||| ||||| ||||| |  ||  | |||||||| || ||||| ||||||||||| || |||||||||||    ||| ||  | || | | | |||     |||    |     ||| | || ||  ||||   || ||||||  ||||  |    | |  ||      |  
TCATCTGTGATAACGGTTGGCGAATGGTTCATTAAGCGCATGCCACTTGTGAAACAAGTTTACTCTGCCTCAAAGCAAATCAGTGCTGCCATTTCTCCAGgtatagcttcttcactattggaaactacaaggtcgtagtggctgtgtttaagaaagcttcgtggt---ttgtgaatt--tatgatttgttaatgcgctgatcatt-

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S51_162V6.1 (Physcomitrella patens), 5'ss of exon 4
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtt----tgatg-gtgggttctgaattcatatggatgagcagtaagccacatgtag
 |  | ||  |   | | || ||||||||||| ||||||||||| ||||| | |||||| || || || || ||||||||||||||||| || ||||| ||||   | |   |  | |||| ||  || |  |  |||| ||||   | |||    | ||  || | |||     |||  || |  |   ||||   | ||    
TCATCCGTGATAATGGTGGGCGAATGGTTCATCAAGCGAATGCCTCTTGTGAAGCATATTTATTCGGCCTCGAAGCAGATCAGTGCTGCTATCTCTCCTGgtacagtttc--ttccagcatcgtt-aacttcatgttagtcatagttgtgttgtcctaatttgttgattcgctgatcac-tgtagaactggtaaaaaagatccc-

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ37288 (Selaginella moellendorffii), 5'ss of exon 5
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag
||  | ||| |   | | || || ||| | || || || ||||| || || || || |||||||| || |||||||| ||||||||||| || ||||||||||||    || |  |   || |   | || || ||        || |   ||       |                                       
GCGTCGGTTCTTATGGTCGGCGAGTGGGTTATCAAACGTATGCCTCTCGTGAGACACATATACTCGGCGTCCAAGCAAATCAGTGCTGCGATCTCTCCAGgtatgaggaacttcgcacgatggattagtttgatttgctttgctaatgttctttcctacag---------------------------------------

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ27661 (Selaginella moellendorffii), 5'ss of exon 4
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag
||  | ||| |   | | || || ||| | || || |||||||| || || || || |||||||| || |||||||| ||||||||||| || ||||||||||||    || |  |   || |   | ||    ||| || |  |     |   |  |                                          
GCGTCGGTTCTTATGGTCGGCGAGTGGGTTATCAAACGAATGCCTCTCGTGAGACACATATACTCGGCGTCCAAGCAAATCAGTGCTGCGATCTCTCCAGgtatgaggaacttcgcacgatggattagttttgcttt-gctaatattctttccaacag------------------------------------------

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|254330499|gb|GR841764.1|GR841764
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|254349027|gb|GR860299.1|GR860299
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|9564106|gb|BE473615.1|BE473615
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|151407101|gb|EV276916.1|EV276916
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|151397141|gb|EV267014.1|EV267014
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|151405159|gb|EV274973.1|EV274973
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|254330500|gb|GR841765.1|GR841765
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|31466200|gb|CD408228.1|CD408228
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTGACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|31459279|gb|CD401307.1|CD401307
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
EST: gi|31561519|gb|CD487357.1|CD487357
EST:     TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAG                         ATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG
genomic: TAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctcta ... tccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcatagtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC