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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg...

Basic information

species Glycine max
transcript GLYMA06G13760.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g02380.2 (Oryza sativa), 5'ss of exon 1
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg
| |  ||||||  ||||||||  |||||||||  ||| ||||||    || ||||| |||||||||||||||||| || ||||||| |||||||||||| |||    ||  |||||  | |||| |  |   |  |  ||  ||    |      || ||  |   ||| | |    | |                    
GGGCTGGAGCTCGGCAAGAGCGCCAAGGACCGGGTCACCACCTCCCAGGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtatg--tcattcttcgat-tcttggcgcattttcgtcct--cccggatctgggattcatggctttcatcaatcttgtgcag------------------

upper sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G064563_T03 (Zea mays), 5'ss of exon 1
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatc---tgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg-------------------------
| |   |||||  ||||||||  |||||||||  ||  |||| | ||||||||||| |||||||||||||||||| || ||||||| |||||||||||| ||||    |   |  || | ||| | |   |    | ||||||     |       |  ||  | |    ||   |||   | |    | |  |      |||                         
GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACCACCTCCGCATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccccgtccctcccctccccttctttagtttagatctgcgaacgccgttgtggttggttc--tgatggtttcgcctgttgcctgccctcccgcctcgaatggggacgggtttgttcgtgcag

upper sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G077669_T01 (Zea mays), 5'ss of exon 1
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg
| |   |||||  ||||||||  |||||||||  ||  |||  | ||||| ||||| |||||||||||||||||| || ||||||| |||||||||||| ||||    |   |||| ||    | | ||   ||     | |  ||      | || |  |    |       | ||   |       |||  |  |   
GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacg--ccctccttcccttctcttgttcggttcctcgtttagatctgcgaacgctgtggtggttctgaatgatgatggttgggacggattcgtgcag--

upper sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 5'ss of exon 1
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacag-atctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg
| |  |||||| ||||||| ||||||||| ||||||||||| ||||| || |||||||| ||||||||||| || ||| | |||||||| |||||||||||||||    |  ||   ||||||||       | |     |   ||  ||       | |   |     |||  || | | ||  |   || |  || | |
GCGTTGGAGCTTAGCAAGAACAACAAGGATCGAATCAACACTTCTTCAGCTTTCAATTCTTTCAAGAACAATTATCTCCTTGTCTATTCGCTCATGATGGgtacaatggccttcccttctctcttcatctttccctttgtttgtctagttatgtctgtcaaaac-ttatttatatcctgtttcgatccgatctggttgttg

upper sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 5'ss of exon 1
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactc-agatctaacc--tcatttccctctttattccacccattacttcatttctcattttcatttttttatcg
|| |  ||||| ||||||| ||||||||||||| |||| ||| |  | || |||||||| ||||||||||| || ||  | ||||| || ||||||||||||| | ||   ||   || |    | ||    || |||||| ||   |  |||   | |  |||       || |   ||| |  || | |  | |  | |  
GTTATTGAGCTCAGCAAGAACAACAAGGACCGAGTCAATACCACCACGGCTTTCAATTCTTTCAAGAACAATTATCTTCTTGTCTACTCTCTCATGATGGgtaaaaat---tcaaatcccaggaaaatggtttctagatctgactagtgttttgtttttccattgtggatcttgcgcaattgcggatctgctgtgtcatgtgt

upper sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
lower sequence: PP1S18_8V6.2 (Physcomitrella patens), 5'ss of exon 1
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg
|    |||| |  | |||     ||||||||| |||| ||| ||||| || |||||| |||||||||||||||||||  ||||||| || || ||||||||||   | | || ||    ||         | ||   |||  ||||  |      |||  |   |   |  |||  ||| ||  |  | |   |  |  |
GCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttccctctgtctttctttttcttttcttttctctttgtttttctgtaccgtccgtaaactg

upper sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
lower sequence: PP1S18_8V6.1 (Physcomitrella patens), 5'ss of exon 1
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg---------------------------------------------
|    |||| |  | |||     ||||||||| |||| ||| ||||| || |||||| |||||||||||||||||||  ||||||| || || ||||||||||   | | || ||    ||         | ||   |||  ||||  |      |||  |   |   |  |||  ||| ||  |  | |   |  |  |                                             
GCCCTGGAGTTTGGGAAGTCTGGCAAGGACCGGATCACCACGTCTTCTGCTTTCAATGCCTTCAAGAACAACTACCTGGTCGTCTACTCGCTTATGATGGgtaacaaaccgttttgcaacttagcctgggattcgcgtcttccctctgtctttctttttcttttcttttctctttgtttttctgtaccgtccgtaaactgtataagaattgttcaccgtgtagtctaccctacgcatatgaccag

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|193340542|gb|FK308289.1|FK308289
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|208238558|gb|GE039030.1|GE039030
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|209711297|gb|BW683622.1|BW683622
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|15813823|gb|BI786098.1|BI786098
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTTCTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|298175985|gb|HO015390.1|HO015390
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|254342363|gb|GR858525.1|GR858525
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|209715234|gb|BW668562.1|BW668562
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|192322278|gb|FK014519.1|FK014519
EST:     ATTCAATTCCTTCAGGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|213601393|gb|DB968709.1|DB968709
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|18041240|gb|BM309534.1|BM309534
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|209709210|gb|BW657179.1|BW657179
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|208285948|gb|GE087420.1|GE087420
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|19453079|gb|BM954489.1|BM954489
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATTTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|208111288|gb|GD910070.1|GD910070
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|213587653|gb|DB971376.1|DB971376
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|298198016|gb|HO039555.1|HO039555
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|209701782|gb|BW667407.1|BW667407
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
EST: gi|209715146|gb|BW665621.1|BW665621
EST:     ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGG                         CTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG
genomic: ATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatct ... atggctatagCTGGAGATTGGCTACAAGGTCCATATGTCTACTACCTTTACAGTACATATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC