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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagataaactcacta...

Basic information

species Glycine max
transcript GLYMA01G42950.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g44630.2 (Oryza sativa), 5'ss of exon 3
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaactttaagccaaagtgtgtaaacaggtttattagctaggta--gaagagataaactcacta----
||| || ||||| |||||||||||||||||||| || || || |||||||||||||| ||||||||||||||||| || || || ||||| || ||||| |||   || | ||  |||| | |  | |    || |||| || || | |    |||  ||     |  | || || || | |  |     |  || |||  |    
TGACGGTCTTGGTGCTGAGATTGTTGGCACCTTCATCCTGGTCTACACCGTCTTCTCAGCCACTGATGCCAAGAGGAATGCCAGGGACTCACATGTTCCTgtaagtatccttctcctttttgcagtgtg---atatgtgaaagttca-gtagtagttagtg--tggtctaatgagttatgcactgtgataactaattcatcaccaa

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 5'ss of exon 1
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctc----ttctcatttgtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagataaactcacta
 || ||||| || || ||||| || |||||||| || || || |||||||||||||||||||| || |||||||| ||||| || ||||| |||||||||||    || |    |  | || |  |     |||  |  ||      |||   |     | ||       | || ||   |   |    | |||   | |||  
CGACGGCCTCGGCGCCGAGATCGTCGGCACCTTCATCCTCGTCTACACCGTCTTCTCCGCCACCGACGCCAAGAGGAACGCCAGGGACTCCCACGTTCCGgttagtataccaactactactgcagtaaagattcagagatggaagtatttttactgttttctgagtgattgatttttgttttaatttgcgcgatcttc-cacag

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 2
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaactttaagccaaagtgtgtaaacaggttta--ttagc-taggtagaagagataaactcacta-
|||||||||||| |||||||||||||||||||| || || || |||||||||||||| ||||| ||||||||||| || || || ||||| || ||||| |||   | || ||  ||| | | |   | ||  ||||| ||  | | |       ||  |  |   ||||   |||||  |  || | |  ||  | |||    
TGATGGCCTTGGCGCTGAGATTGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCAGCCACCGATGCCAAGAGGAATGCCAGGGACTCCCATGTTCCTgtaagtactcttccacttcccttt---tcctagtttgttcagttgtta-tagttctgcttggattagtttggcttagcacacatatatgtaattgaatcaactt

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 2
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaact-ttaagccaaagtgtgtaaacaggtttattagctaggtagaagagataaactcacta-
 || |||||||| || ||||| ||||||||||| || || || |||||||||||||| ||||| ||||||||||| ||||| || ||||| || || || |||   | || || || ||  ||  | | ||  ||||| || || ||| |     |  || |  ||  |||           | |  |||| |      || 
GGACGGCCTTGGCGCAGAGATCGTTGGCACCTTCATCCTAGTCTACACCGTCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactcttcgtcctt--tcgttttcctagtttgttcagctgttagggttctgcttgaattcacatttgcatatctaaaatataagatgacggttgtaa

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G174807_T01 (Zea mays), 5'ss of exon 2
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaactttaagccaaagtgtgtaaacaggtttat--tagctaggtagaagagataaactcacta
 || ||||| || || ||||| || |||||||| || || || |||||||||||||||||||| || |||||||| ||||| || ||||| || || |||||    |  ||  |||   |||  ||     | | |  ||  | |    ||        |  ||   |  ||  |  ||  || || || || |||      
CGACGGCCTAGGCGCCGAGATCGTCGGCACCTTCATCCTCGTCTACACCGTCTTCTCCGCCACCGACGCCAAGAGGAACGCCAGGGACTCCCATGTGCCGgtgagta--cagtatcagccttgccttcctgcttattcgcctcgtccgtccgtgcaagctcgacttatcgatggtttctttgtggacga-atgaacag----

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 2
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttc--tctcttctcatttgtgcaactttaagccaaagtgtgtaaac--aggtttattagctaggtagaagagataaactcacta
 ||||| ||||| |||||||| |||||||| ||| ||||||| ||||| || ||||| || ||||||||||||||||| || |||||||| || || || |||   |||   | || || |    |||||    || | ||||  | |  |      | | || |   |  ||| | |  |||||| |     | |  ||    
CGATGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTTTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTCCCTgtaagtattttccctcattgtatcatctctctgtatgtatgcatatgtgtggtttgttttatagatctaactttgtcaa-taggtaaagcgattgagttct---

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 5'ss of exon 2
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaactttaagccaaagtgtgtaaacaggtttattag--ctaggtagaagagataaactcacta
|||||||||||| ||||||||||||||||||||  ||||||||||||| |||||||| || |||||||||||||||||||| |||||||||||||| || |||   |||| || | ||||||        ||||  |  || | ||    || | | ||     |  ||  || |       |        |   |||| | 
TGATGGCCTTGGTGCTGAGATTGTTGGCACCTTCGTTCTTGTTTACACTGTCTTCTCTGCTACTGATGCCAAGAGAAACGCCAGAGACTCTCACGTCCCTgtatgtattc-tcttatttctttctcaacttcatgagaccatccttgtttcatattatgattttactttccttggaatcttattttttgttttttctcatt-

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 2
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaactttaagccaaagtgtgtaa--acaggtttattagctaggtagaagagataaactcacta
|| ||| ||||| |||||||| |||||||| ||| ||||||| ||||| ||  |||| || ||||||||||||||||| || |||||||| || ||||| |||   |||| ||    |   | | | | |  |  | ||    |||      |  | | ||   | |  ||| || |  |  | | | || | |     || 
TGCTGGGCTTGGTGCTGAGATAGTTGGCACTTTTGTTCTTGTCTACACTGTTCTCTCTGCAACTGATGCCAAGAGAAATGCCAGAGACTCACATGTTCCAgtaagtattc-tctctctgtgtatatatacataaatatgtgggttttgttttacatatctagttatatatttctttgtcaattggtaaag-tgattgagctg

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ18960 (Selaginella moellendorffii), 5'ss of exon 2
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtac----------ccattcatcatctttctt--ctctcttctcattt-gtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagataaactcacta----------------------------------------------------------------------------------
 ||||| |||||||||||||||||||| |||||  |||| || ||||| ||||||||||||||||||||||||||||  || |||||||| || || |||||||          |||| ||     ||  ||   || | ||||||   ||    ||||    |    | | |      ||   ||  |||| |      | |  |||  ||                                                                                   
AGATGGTCTTGGAGCTGAGATTGTTGGTACCTTCGTTCTCGTCTACACGGTCTTCTCCGCCACTGATGCCAAGAGAAGTGCCAGAGACTCCCATGTCCCGgtacgtttcttcttccatccaaagctttggttgattcccctctcatgaagttttgcttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacag

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ11572 (Selaginella moellendorffii), 5'ss of exon 2
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtac------ccattcatc---atctttc-----ttctctcttctcattt-gtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagataaactcacta----------------------------------------------------------------------------------
 ||||| |||||||||||||||||||| |||||  |||| || ||||||||||||||||||||||||||||||||||  || |||||||| || || |||||||      || | ||||   | ||||      ||| | | ||||||   ||   |||||    |    | | |      ||   ||  |||| |      | |  |||  ||                                                                                   
AGATGGTCTTGGAGCTGAGATTGTTGGTACCTTCGTTCTCGTCTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAGTGCCAGAGACTCCCATGTCCCGgtacgtttctccttccatccaaagctttggttgattcccccctctcatgaagttttacttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacag

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|192305304|gb|FG997556.1|FG997556
EST:     ATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: ATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|193443247|gb|FK405255.1|FK405255
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTGGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCT-CCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|192297908|gb|FG988364.1|FG988364
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTT
EST: gi|192295284|gb|FG985938.1|FG985938
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|4313282|gb|AI460401.1|AI460401
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTNTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTG-TCCACTTG-CT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|151394697|gb|EV264568.1|EV264568
EST:     TCTTCTCCGCCACTGATGCCAAGAGAGACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|193424732|gb|FK388131.1|FK388131
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|192312379|gb|FK003171.1|FK003171
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTT-GGTC
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTC
EST: gi|192312380|gb|FK003172.1|FK003172
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTG
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTG
EST: gi|193571986|gb|FK532349.1|FK532349
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTGGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|31474331|gb|CD416359.1|CD416359
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTCCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|208110953|gb|GD910967.1|GD910967
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
EST: gi|151403754|gb|EV273564.1|EV273564
EST:     TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCG                         ATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT
genomic: TCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattc ... aaaattgtagATTTTGGCCCCTCTTCCAATCGGGTTTGCTGTGTTTTTGGTCCACTTGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGCCTTGGAGCTGAGATTGTTGGCACCTTTATTCTTGTTTACACCGTCTTCTCCGCCACTGATGCCAAGAGAAACGCTAGAGACTCTCACGTTCCGgtacccattcatcatctttcttctctcttctcatttgtgcaactttaagccaaagtgtgtaaacaggtttattagctaggtagaagagataaactcacta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcttc