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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttcatttcaccattttctcctctttcgtctcccattcatgctctaaaactgattcgtacttttccttctgcag

Basic information

species Glycine max
transcript GLYMA08G02420.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttcatttcaccattt-tctcctctttcgtctcc-cattcatgctctaaaactgattcgtacttttccttctgcag------------------
||||||||| || ||| | ||||| |||||||||||||| ||||||||||||||||| || ||||| || ||||  |||||||| ||||||||||| |||||   |  | |   | ||  |   |||  || ||  |  | | |  | |||     |    |    |      | || | ||                  
GAACGACGCCGATGTCGCCAAGCAGATCCAGCAGATGGTGCGGTTCATCCGCCAGGAGGCCGAGGAGAAGGCCAGCGAGATCTCCGTCTCCGCCGAGGAGgtcagtacttacccctcccctcgcctcgcctctcccccgcgcgtcgaagcttcgggaagcctctcgatccgcgcctccgaagcttttcacccgcccgatc

upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G070360_T01 (Zea mays), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgt----ttctcttcatttcaccattttctcctctttcgtctcccattcatgctctaaaactgattcgtacttttccttctgcag-----------------
||| ||||| || ||  | ||||| |||||||||||||| ||||||||||||||||| || || || || ||||| |||||||| ||||||||||| |||||    ||  ||||  | |  | |  || ||    | |   |      | || |  | | || ||    || | | ||| || |                 
GAATGACGCCGATGTAGCCAAGCAGATCCAGCAGATGGTGCGGTTCATCCGCCAGGAGGCCGACGAGAAGGCCAACGAGATCTCCGTCTCCGCCGAGGAGgtcagttttccttcgctgccgcttcctcaccctcctagaagcttccagaagcccctaga-tggttgcctctgtactttcagctgcccgatgtggctggcgc

upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G030167_T01 (Zea mays), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtt--tctcttcatttcaccattttctcctctttc----gtctcccattcatgctctaaaactgattcgtacttttccttctgcag--------------
||| ||||| || || || ||||| |||||||||||||| ||||||||||||||||| || || || || ||||| |||||||| ||||||||||| |||||   | |   |      ||  || |||  | | |      || |||           |  ||  |   |    |  |  ||||                
GAATGACGCCGATGTATCCAAGCAGATCCAGCAGATGGTGCGGTTCATCCGCCAGGAGGCCGACGAGAAGGCCAACGAGATCTCCGTCTCCGCCGAGGAGgtcagtttaccctgcctgccgcttcctcaccctcctagaagcttccagaagcttctagatgcttgtctctgtactctcagctgcccgatctggctgacgc

upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G64200.1 (Arabidopsis thaliana), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtt--tctcttcatttca-ccattttctc-----ctctttcgtctcccattcatg-ctct----aaaactg-------attcgtacttttccttctgcag
||||||||| || |  || |  || ||||||||||||||| |||| |||||||||||||| || ||||| || || ||||||||  ||||| | ||||| ||   ||  | |||| || ||| | |||      |||  || |  |  || | || ||||    | || ||       |||     || | ||| || | 
GAACGACGCCGATGCTTCCATCCAGATCCAGCAGATGGTTAGGTTTATCCGCCAGGAAGCCGAAGAAAAGGCTAACGAGATCTCCATCTCCTCTGAAGAAgtaagtccatacattacatccactctcttttgatctcgatctttacgaatacgtgactctgttgacaattgcgtgactattttggtttgttcttttgaaa

upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv02s0025g01000.t01 (Vitis vinifera), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtt--tctcttcatttcaccattttctc-ctctttcgtctcccattcatgctctaaaactgattcgtacttttccttctgcag-----------------
|||||||||||| ||||| ||||| ||||||||||||||  | ||||||||||| ||||| |||||||| || ||||| |||||||| ||||||||||| ||    ||  ||| |  |   | | ||| || |||  ||| |   || |    |   |   | | | |           | |                  
GAACGACGCAGATGTCTCCAAGCAGATCCAGCAGATGGTGAGATTCATCCGCCAAGAAGCGGAGGAAAAGGCGAATGAAATCTCTGTATCCGCCGAAGAAgtaagcctactcactcaaatgtgtactctcttttttctcttcggatcgtttggtgctaggaaattgcaagaaaatcagaggaaggaaaaaaaattaaaaa

upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S269_15V6.1 (Physcomitrella patens), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgttt--ctcttcatttcaccattttctcctctttcgtctcccattcatgctctaaaactgatt-cgtacttttccttctgcag-----------------
|||||||   || || ||  ||||| ||||||||||||| | |||||| ||||||||||| ||||| || ||||||||||||||||| || ||||| |||||    |  |     ||      | | ||     ||| | | | |  |  | ||     | ||   |  |||      | | |                 
GAACGACATGGAGGTTTCGCAGCAAGTCCAGCAGATGGTGCAGTTCATACGCCAGGAAGCGGAGGAGAAGGCCAATGAGATCTCTGTATCTGCCGAGGAGgtaagaccatcaggctccttgaatccaccgggcacgtttgcaaatgtttttataggggagtttatctgttttggagaattcggacctcgaatcgacgttg

upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S68_127V6.1 (Physcomitrella patens), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgt----ttctcttcatttcacc-----attttctcctctttcgtc------tcccattcatgctctaaaactgatt--cgtacttttccttctgcag---
|||||||   || || || |||||  ||||||||||||| | |||||||||||||||||| ||||| || ||||| ||||||||||| || || ||||||||    |||| | || |   ||      |||    |  ||  ||       |  |  |  ||     || |||| |  ||   |     |  |  ||   
GAACGACATTGAGGTTTCGAAGCAGGTCCAGCAGATGGTGCAGTTCATCCGCCAGGAAGCAGAGGAGAAGGCCAACGAGATCTCTGTATCTGCTGAAGAGgtgaagttctttacaatgtcccttgtggtttcaggcgattctgttgaggggtttctctattgtgaagaatctgaatgtcgagttaaaaatcttataggtt

upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ17636 (Selaginella moellendorffii), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttcatttcaccattttctcctctttcgtctcccattca--tgctctaaaactgattcgtacttttccttctgcag--------------------
|||||| || || ||| | |||||  ||  |||||||||  | ||||||||||||||||| ||||| |||||||| |||||||| |||||||| ||||||||     ||  | |   | |  ||| || | | | ||   | | |  || |  |    ||  | |    |||||||| |  |                    
GAACGATGCCGAGGTCGCCAAGCAGGTCGCGCAGATGGTGAGATTCATCCGCCAGGAAGCCGAGGAGAAAGCCAACGAGATCTCGGTCTCCGCAGAAGAGgtaaggttt--tcttctcctcctcttctttgtagacttggaataaattgatagatggatggatgggttctttccttcggtggagctgacattggatttccag

upper sequence: GLYMA08G02420.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ29103 (Selaginella moellendorffii), 5'ss of exon 1
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttcatttcaccattttctcctctttcgtctcccattca--tgctctaaaactgattcgtacttttccttctgcag--------------------
|||||| || || ||| | |||||  ||  |||||||||  | ||||||||||||||||| ||||| |||||||| |||||||| |||||||| ||||||||     ||  | |   | |  ||| || | | | ||   | | |  || |  |    ||  | |    ||||||||||  |                    
GAACGATGCCGAGGTCGCCAAGCAGGTCGCGCAGATGGTGAGATTCATCCGCCAGGAAGCCGAGGAGAAAGCCAACGAGATCTCGGTCTCCGCGGAAGAGgtaaggttt--tcttctcctcctcttctttgtagacttagaataaattgatagatggatggatgggttctttccttctgtggagctgacattggatttccag

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|15663576|gb|BI700947.1|BI700947
EST:     GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAATAAGACC
genomic: GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|207720108|gb|GD702607.1|GD702607
EST:     GGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAGGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|208327231|gb|GE122397.1|GE122397
EST:     GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|13252165|gb|BG363068.1|BG363068
EST:     GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|208182348|gb|GD980683.1|GD980683
EST:     GCCAATGAGAATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GCCAATGAG-ATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|6455236|gb|AW185919.1|AW185919
EST:     GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|208225425|gb|GE025424.1|GE025424
EST:     GGAAGCTGGAAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GGAAGCT-G-AGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|7639786|gb|AW734101.1|AW734101
EST:     GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|193378853|gb|FK345194.1|FK345194
EST:     GGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
EST: gi|5605982|gb|AI900080.1|AI900080
EST:     GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAG                         GAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC
genomic: GCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttc ... ccttctgcagGAATTCAATATCGAGAAGCTGCAGTTAGTCGAAGCCGAGAAGAAGAAGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACGACGCAGACGTCTCAAAGCAAATCCAGCAGATGGTTCGGTTCATCCGCCAGGAAGCTGAGGAAAAAGCCAATGAGATCTCTGTCTCCGCCGAAGAGgtttctcttcatttcaccattttctcctctttcgtctcccattcatgctctaaaactgattcgtacttttccttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA