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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgagttttgctcttttgaaacaaattttttgttggtttgaatgtttgctttaggatggaatgaatttggatctgagggaagagaggttcttaaa...

Basic information

species Glycine max
transcript GLYMA09G40650.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 5'ss of exon 3
AATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgagttttgctcttttgaaacaaattttt--tgttggtttgaatgtttgctttaggatggaatgaatttggatctgagggaagagaggttcttaaa---
||| | || |||||||||||||| || || |||||||| ||||||||||||||||| ||||||||||| ||||| ||| | ||||| |||||||||||||||| |   | |    ||| |||  | ||  |  |   || |    ||  ||  |  |||  |     |    |||  |    |   | |      |||  ||   
AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaag---aatccaactccttttcatcacttcatgaatgatatcatggctgaatagtttctgtgatcacactttttaaat--atatatgtttctctctataatgc

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 5'ss of exon 3
AATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgagttttgctcttttgaaacaaattttttgttggtttgaatgtttgctttaggatggaatgaatttggatctgagggaagagaggttcttaaa-------
||| | || |||||||||||||| || || |||||||| ||||||||||||||||| ||||||||||| ||||| ||| | ||||| |||||||||||||||| |   | |    ||| |||  | ||   ||  || || | | |  |     |      ||  || |   |   | | |    | |    |   |  |       
AATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaag---aatccaactccttttcatca--cttcatgatgatatcatggcggaatagtttctgtgatcacactt--tttaaatatatatttttctctctataataca

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G099754_T01 (Zea mays), 5'ss of exon 3
AATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgagttttgctcttttgaaacaaattttttgttggtttgaatgtttgctttaggatggaatgaatttggatctgagggaagagaggttcttaaa-----
||| ||||||||||||| || || || || |||||||| ||  |||||||||| || ||||||||||| ||||| ||| | ||||| ||||||||||||||||   |   || ||||| | | |  |   || |  |   || ||||||    | | |    |    |   |   |  |        |  |  |  |        
AATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCATGTTTCGAGGAAGTCTAGAAAACCACTTATTCCGAAgtaaacc---ttctgctcctgttatgctgtttgtcag--agtgtgaatgacatcatcaccgagttcagtgctgccacttttttacttaatgtcttctgttttccc

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G007283_T02 (Zea mays), 5'ss of exon 3
AATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgta---cggcgagttttgctcttttgaaacaaattttttgttggtttgaatgtttgctttaggatggaatgaatttggatctgag-ggaagagaggttcttaaa
||  ||||||||||||| || || || || |||||||| ||  |||||||||| || ||||||||||| ||||| ||  | ||||| ||| ||||||||||||   |  | | |  || |  |     |  | |  ||  |||||  |||   ||| ||| |  ||     |  | | | || |  ||       |||||    
AACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttctactcctgtttgtcctggatgattgcttgcttggt--gaactgttgattttgcttgattacaggtggtacctaactggcttttctgttctct--

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 5'ss of exon 3
AATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgagttttgctcttttgaaacaaattttttgttggtttgaatgtttgctttaggatggaatgaatttggatctgagggaagagaggttc-ttaaa----
||||||||||||||||| ||||| ||||| || || |||||| || |||||||||| ||||| ||||||||||| ||  | ||||||||||| || |||||||||    ||| |  |   ||    | || |  ||  |  ||| |   |||   ||||  | |   ||||   |||      |        ||| || ||    
AATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTATGTTCCGAGGAAGCCTCGAAAATCACTTGTTTCGAAgtacgctccgttctttttgcttt--gccaaatgattactaatttaagccttt---ttagcttagcccgaatcaagatggacttgtttctctattcattgaatgcg

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|193434778|gb|FK403296.1|FK403296
EST:     AGTTTAGGAAAATCACTTATTCCG-A                         AGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
genomic: AGTTT-GGAAAATCACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
EST: gi|193413383|gb|FK379158.1|FK379158
EST:     TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAA                         AGGCAACTGTCCCTTTATCATGGGCTA
genomic: TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTA
EST: gi|193686874|gb|FK629949.1|FK629949
EST:     ACTTATTCCGAA                         AGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
genomic: ACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
EST: gi|193711858|gb|FK648769.1|FK648769
EST:     TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAA                         AGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
genomic: TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
EST: gi|208178448|gb|GD977463.1|GD977463
EST:     TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAA                         AGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
genomic: TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
EST: gi|207774261|gb|GD743719.1|GD743719
EST:     TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAA                         AGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
genomic: TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
EST: gi|193444433|gb|FK409787.1|FK409787
EST:     TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAA                         AGGCAACTGTCTCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
genomic: TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
EST: gi|208189735|gb|GD987751.1|GD987751
EST:     TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAA                         AGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
genomic: TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
EST: gi|207790347|gb|GD760364.1|GD760364
EST:     TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAA                         AGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG
genomic: TGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgag ... atgcttccagAGGCAACTGTCCCTTTATCATGGGCTACAAGAATGATGATTGCTCTTGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCATGTTCCGAGGGAGTTTGGAAAATCACTTATTCCGAAgtacggcgagttttgctcttttgaaacaaattttttgttggtttgaatgtttgctttaggatggaatgaatttggatctgagggaagagaggttcttaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacaaa