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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaacttaatctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag

Basic information

species Glycine max
transcript GLYMA17G13440.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 10
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaacttaatctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag---------
|| | ||| ||||||||||| || ||||| |||||||||||||| |||||||| |||||| ||||||| || |||   | |||| | || || |  ||||| ||  |   || ||  | |    ||    |   |      | | |  ||     || |||| |||||||||  | ||  ||||            
GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgctgtccttg--atccgtctcattgtcagtaagcattcacagcattggggattagtaggtattgtgtgct-catttgttgcttgtatgtag

upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G179308_T03 (Zea mays), 5'ss of exon 9
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaacttaatct-caattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag-----------------------
|| |  ||  | || |||||||||||||| ||||| ||||| || |||||||| ||||| ||||| || || ||| | |  ||||| ||||| |  ||||| ||  ||| | ||     | ||   |    || |  |  |      || ||| | || |||   | |    ||  |   |||| | |                       
GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttcatgcaattgtctcatatcatatgcttaagagggcagggttatctga-acatcagtgc-tgtgagatctggtcgatgtcttgtgcttattaatccttgtttgtag

upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 10
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaacttaatctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag-----------------------------
|| | ||| |||||||||||||| || ||| ||||||| ||||||||||||||||||||  | |||||| | || |||| |||| |||||||||| |||| ||||| || |  ||   || |     || ||     |  | ||| || | ||   |  || | |  |  || ||  |   ||||                               
GGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGAgtgagtgatat-cattgaagacatttctgcagttttcaaaatcataatattttatgcctttgtctttgcta-gtgat-tagtagtttgactttttattaattgtcatgtgtttttcag

upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 5'ss of exon 10
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacatac-catgcgaacttaatctcaa-ttgattgatcct---------taaaatatgataaataagtatgtattgtgtcatgcaaatgtttag----------------------------------------------------------------
|| |  || ||||||||||||||||| |||||||||||| | || ||||||||| | ||  | |||||  | ||    | |||| | ||||| |  ||||||||||||| |   ||  ||  |  |||    ||  |  || ||         | |  | |  | |   |  | || |    |||||   |||  |||                                                                
GGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGAgtaagtgacatgcgtctgttaatcttttcttggcttcctctattctaatcttgtgtgatgtgtattgagccaccaagtttgagttcatgattatgagtagacgttttctatattctgtctgaaagtgtcctttggtttacgagcactttcaacgacctctgcag

upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ32324 (Selaginella moellendorffii), 5'ss of exon 9
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaactta-atctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag
|| |   |  |||||||||||||||||||| | ||||| || || |||||||||||  | || |||||  |  |    | |||  |  | |  || |||||||| | ||       | |  || |   |   ||  | ||||  |   |    |    |                             
GGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTTCCAGACGCATAATCGATAACGTAGAgtaagtcagatttgtactggatctataaaccttgtggctcatccc-acggtgctttgtgcag----------------------------

upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ20929 (Selaginella moellendorffii), 5'ss of exon 7
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaactta-atctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag
|| |   | ||||||||||||||||||||| | ||||| || || |||||||||||  | || |||||  | ||    | |||  |  | |  || ||||||||   ||       | |  || |   |   ||  | ||||  |   |    |  | |                             
GGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGAgtaagtcggatttgtactggatctataaaccttgtggctcatccc-acggtgctttctacag----------------------------

upper sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ20930 (Selaginella moellendorffii), 5'ss of exon 8
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaacttaatctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag
|| |   |  |||||||||||||||||||| | ||||| ||||| |||||||||||  | || |||||  | ||    | |||  |  | |  || ||||||||   ||  |    | |  |     |  |  |  | | |||     |                                      
GGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTTGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGAgtaagtcggatttctactggatctgtaaaccttccac-ggtgctttgtgcag-------------------------------------

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|31469021|gb|CD411049.1|CD411049
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|193703915|gb|FK634803.1|FK634803
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|9204054|gb|BE330278.1|BE330278
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|151400202|gb|EV270016.1|EV270016
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|10843331|gb|BF066634.1|BF066634
EST:     GAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: GAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|21602499|gb|BQ612830.1|BQ612830
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|207825151|gb|GD795056.1|GD795056
EST:     AAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: AAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|23728459|gb|BU762283.1|BU762283
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|22933543|gb|BU550682.1|BU550682
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|207847382|gb|GD820423.1|GD820423
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|15000364|gb|BI321178.1|BI321178
EST:     CCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: CCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|208298173|gb|GE091064.1|GE091064
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|208051460|gb|GD845927.1|GD845927
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|14011042|gb|BG725964.1|BG725964
EST:     GGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: GGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|151400815|gb|EV270629.1|EV270629
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
EST: gi|208123639|gb|GD924541.1|GD924541
EST:     ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA                         CCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG
genomic: ATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgaca ... aaatgtttagCCGACATGCTGAGAAGTATGTTAGAAGGGGTAGATTGGACTGGCCTGAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGAgtaagtgacataccatgcgaacttaatctcaattgattgatccttaaaatatgataaataagtatgtattgtgtcatgcaaatgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA