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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgattaatcctgaagtcctaattgctttaaaagatgcccttgactagttgttttttatgatgcatccttgacaagttctttaagcacttagtaaaattatggttgtaccacttgacattgcag

Basic information

species Glycine max
transcript GLYMA18G01710.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 5'ss of exon 11
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgact--gattaatcctgaagtcctaattgc---tttaaaagatgccctt-gactagttgttttt------tatgatgcatccttgacaagttctttaagcacttagtaaaattatggttgtaccacttgacattgcag-------
                     ||| |||||||||||||||||||| || ||||||||||||||||||   || |  | | |    ||  ||| | ||| |    |    | ||||  |  |  || |  ||||       ||   ||  || |  | |   |    | |   || ||||  |      |  |    ||   | |  |        
---------------------AGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTCGCACTCCGTAAATGCGTTGAGgttaatcattttgcctacataccttgactcttaaatacactggacatgtgtttggtaagttatctactaaaaagtttcctaataaaacaaacag

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 5'ss of exon 11
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgact--gattaatcctgaagtcctaa--ttgctttaa-aagatgc-ccttgactagttgttttttatgatgcatccttgaca------agttctttaagcacttagtaaaattatg--gttgtaccacttgacattgcag-------
                     ||| ||||| ||||| |||||||| |||||||||||||||||||||  |||||  | | |    ||  ||| | |  ||||  ||| || ||||  |  |  ||         ||  |   || |   |        | || |  ||    ||    ||| || |  |    ||   || |   | ||        
---------------------AGTTTTCTCTAGAGAGGCATGGCGTTGTGTGTGGCATATGATTCAGAATGACTTGGTTCACGGTTGGGGTCTTGACTTTGCGCTAAGAAAATGCGTCGAGgttaacatacaaatacaacttattcacaaacgcgtataattttacaaaacgttttcgaaactaagaagaaacactttttaatgattcaataaacag

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttg-actgattaatcctgaagtcctaattgctttaaaagatgcccttgactagttgttttttatgatgcatccttg-acaagttctttaagcacttagtaaaattatggttgtaccacttgacattgcag
 || || ||||| |||||||| || ||||||||||||||||||||||| |||||||||||||| ||||||  ||| | |  |  | |  |  |   | ||| |     |  | |    || |   |  || |    | |  ||| | | |  |   || ||                                     
ATTCGTGGAGATAATGGCTCCTGTATTCTCAAGAGATGCATGGCGCTGCGTGTGGCATATGATCCAGgttacacttact--ttattatctattggctccttca-----tatcttcatataatgtctccttcttgcacctaattgtatatgaaccaaaaacag------------------------------------

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 5'ss of exon 2
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgattaatcctgaagtcctaattgctttaaaagatgcccttgactagttgttttttatgatgcatccttgacaagttctttaagcacttagtaa-aattatggttgtaccacttgacattgcag
|||||||||||| |||||||| || || || |||||||||||||| ||||||||||||||| |||||||      ||  ||||| || |    |     |||  |  | | |      ||||| |     |||    |   |  ||||||       |  |   |   |||||  |                     
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgt----atatatatcctcaaatttaga----attagtaagttctc------agttgctccagttgacctgttactatcaagtttaagtgcctttctatgggaattacag---------------------

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 5'ss of exon 11
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgattaatcctgaagtcctaattgctttaaaagatgcccttgactagttgttttttatgatgcatccttgacaagttctttaagcacttagtaa-aattatggttgtaccacttgacattgcag
|||||||||||| |||||||| || || || |||||||||||||| ||||||||||||||| |||||||      ||  ||||| || |    |     |||  |  | | |      ||||| |     |||    |   |  ||||||       |  |  ||   ||||   |                     
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgt----atatatatcctcaaatttaga----attagtaagttctc------agttgctccagttgacctgttactatcaagtttaagtgcctttctgtgggaattgcag---------------------

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgattaatcctgaagtcctaattgctttaaaagatgcccttgactagttgttttttatgatgcatccttgacaagttctttaagcacttagtaa-aattatggttgtaccacttgacattgcag
|||||||||||| |||||||| || || || |||||||||||||| ||||||||||||||| |||||||      ||  ||||| || |    |     |||  |  | | |      ||||| |     |||    |   |  ||||||       |  |  ||   ||||   |                     
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgt----atatctatcctcaaatttaga----attagtaagttctc------agttgctccaattgacctgttactatcaagtttaagtgtctttctgtgggaattgcag---------------------

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
lower sequence: EFJ04271 (Selaginella moellendorffii), 5'ss of exon 6
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgact-gattaatc-ctgaagtcctaatt---gctttaaaagatgcccttgactagttgttttttatgatgcat--ccttgacaagttctttaagcacttagtaaaattatggttgtaccacttgacattgcag
                     ||| || ||  |  | || ||||||||||||||||||||||||||   ||||| | |  ||  |||  | |   | |   || |  |||  ||  |   |   ||    |||     | | |  | || |  | || ||    || |   |     |||| |||  |               
---------------------AGTTTTTTCGCGCAAGGCCTGGCGCTGTGTGTGGCATATGATTCAAAATGACTTGGTGCATGGCTGGGGACTAGACTTTGGCCTGCAAAAGTGTGC---AACGgtgagctttgccagtactttgctttaattattttttcttacattccatt--cctatgattgagcag-------------

upper sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
lower sequence: EFJ32148 (Selaginella moellendorffii), 5'ss of exon 7
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgact-gattaatc-ctgaagtcctaatt---gctttaaaagatgcccttgactagttgttttttatgatgcatccttgacaagttctttaagcacttagtaaaattatggttgtaccacttgacattgcag
                     ||| || ||  |  | || ||||||||||||||||||||||||||   ||||| | |  ||  |||  | |   | |   || |  |||  ||  |   |   ||    |||     | | |   |   |   | |||    || |        |||| |||  |               
---------------------AGTTTTTTCGCGCAAGGCCTGGCGCTGTGTGTGGCATATGATTCAAAATGACTTGGTGCATGGCTGGGGACTAGACTTTGGCCTGCAAAAGTGTGC---AACGgtgagctttgccagtactttgctttaattatttttgcttacattcctttcctatgattgagcag-------------

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|15661819|gb|BI699190.1|BI699190
EST:     CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTA
genomic: CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTA
EST: gi|192319061|gb|FK010625.1|FK010625
EST:     CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
genomic: CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
EST: gi|193670535|gb|FK609045.1|FK609045
EST:     CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
genomic: CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
EST: gi|192319062|gb|FK010626.1|FK010626
EST:     CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
genomic: CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
EST: gi|193622076|gb|FK568122.1|FK568122
EST:     CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
genomic: CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
EST: gi|254315636|gb|GR825445.1|GR825445
EST:     AGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
genomic: AGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
EST: gi|254347136|gb|GR856806.1|GR856806
EST:     CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
genomic: CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
EST: gi|208265459|gb|GE062651.1|GE062651
EST:     CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
genomic: CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT
EST: gi|192302164|gb|FG995816.1|FG995816
EST:     CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG                         AATGACTTGGTCCACGGGTGGGGTTTTGATTTTGCTTTTAGAAGATGTGTT
genomic: CTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgat ... gacattgcagAATGACTTGGTCCACGGGTGGGGTCTTGATTTTGCTCTTAGAAGATGTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgattaatcctgaagtcctaattgctttaaaagatgcccttgactagttgttttttatgatgcatccttgacaagttctttaagcacttagtaaaattatggttgtaccacttgacattgcag

- - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - GAGATG