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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattctacttcttcttcatacacaacaccaccaccttaacctaattggagacataaggttcgtctacgggagaagagaaggggaagagatcgcgg...

Basic information

species Glycine max
transcript GLYMA14G40430.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40430.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os12g10560.1 (Oryza sativa), 5'ss of exon 2
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaat--tctacttcttcttcatacacaacaccaccaccttaacctaattggagacataaggttcgtctacgggagaagagaaggggaagagatcgcgg
||||| ||||| ||| |||||||  ||||||| ||||| || || ||||| |||||||| || |||||||| || |||||||||||||| || |||||||| |      || |           | ||      | |    |  |  |    |    |||  || || | |   ||                         
ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAGgtgagggggatccagcaaaggagattccatcttggcgctggttcgatttgtgggtgttcatctgggtcttttcttggtcgcag-------------------

upper sequence: GLYMA14G40430.1 (Glycine max), 5'ss of exon 2
lower sequence: AC195874.2_FGT002 (Zea mays), 5'ss of exon 2
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattctacttcttcttcatacacaacaccaccaccttaacctaattggagacataaggttcgtctacgggagaagagaaggggaagagatc-gcgg
||||| ||||| ||| |||||||| ||||||| ||||| || || ||||| || ||||| || |||||||| || || ||||||||||| ||||||||||||| |    |||   |   |  | |      |  |    ||  | | |||            |||  ||      ||   |          | |  || |
ATCCGCTTCATCCTGCTGCAGAACCGGCAGGGGAAGACTCGACTGGCCAAGTATTACGTCCCGCTCGAGGACTCGGAAAAGCACAAGGTTGAATACGAGgtaagagacgtacgaatcagtggtgc-tggttcggctcggtt--cttgattttctgttctgttttctccttttcttgatttggtttcttgctggtttgcag

upper sequence: GLYMA14G40430.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G052713_T03 (Zea mays), 5'ss of exon 2
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattctacttcttcttcatacacaacaccaccaccttaacctaattggagacataaggttcgtctacgggagaagagaaggggaagag--atcgcgg-----------------------------
||||| ||||| ||| |||||||| ||||||| || || || || ||||| ||||| ||  |||||||||| ||||||||||||||||| || |||||||| |   | ||      |  |  |  | || |  |  |  | | | | ||    ||     | | |||||  |      | |  |  ||       | || |                             
ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGgtgagcctgctggac--tgctggtggagaaga--aagatttgatcttgatgccggattctggttccgtctttgatttgggcggtgctgactccctgttgctgtttcttggccttggttgtggtgaatccag

upper sequence: GLYMA14G40430.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G47830.1 (Arabidopsis thaliana), 5'ss of exon 2
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattctacttcttcttcatacacaacaccaccaccttaacctaattggagacataaggttcgtctacgggagaagagaaggggaagagatcgcgg
|||||||||||  | ||||||||||| || || ||||| ||||| ||||||||||| || |||||||| || |||||||| ||||| || ||||||||||||  | |   | |||   ||| ||  || |  |      ||| |||  || |     | |   |    |        ||                    
ATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAGgtactactc--atttcaaattc-tat-catcttcctttttttatcctttttaggtttctgattcttaattcttttcacag--------------------

upper sequence: GLYMA14G40430.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv04s0023g03340.t01 (Vitis vinifera), 5'ss of exon 2
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattctacttc-----ttcttcatacacaacaccaccaccttaacctaattgga-gacataaggttcgtc-tacgggagaagagaaggggaagagatcgcgg
|||||||||||  ||||||||||||||||||| ||||| ||  | ||||| |||||||||||| ||||||| || ||||| |||||||| |||||||||||     |  |  |||     |   || |     ||      |  ||  | |  |     |   |||  || ||  | |    |   | |      |    | || |
ATCCGATTCATATTGTTGCAGAACAGGCAGGGAAAGACTCGATTAGCCAAGTACTACGTTCCTTTCGAGGAATCTGAGAAACACAAGGTCGAATACGAGgtgggtttcttctttccgatctctctctttgtttacttatttattttttctttctcaactggtttaaattttgttgttctttggttcaaatttttcattctttgcag

upper sequence: GLYMA14G40430.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 5'ss of exon 3
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattctacttcttcttcatacacaacaccaccaccttaacctaattggagacataaggttcgtctacgggagaagagaaggggaagagatcgcgg
|||||||||||  |  | ||||||||||||||||||||||| || ||||| ||||| |||||||| || || ||||||||||||||||| ||||||||||||  |  ||  |||  | ||| | | |    | ||    ||  | |  | ||      || |||  | |   | ||                       
ATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAGgtatta--tcctcttgattttcct-ctctcttctacggtttt--ctttctagggttttgaatgttattgtcttgtag-----------------------

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|6846408|gb|AW348698.1|AW348698
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|58022169|gb|CX708910.1|CX708910
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|298170111|gb|HO018735.1|HO018735
EST:     AATACTGCGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|4297809|gb|AI442671.1|AI442671
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|33388323|gb|CA851530.1|CA851530
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTCGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|15661937|gb|BI699308.1|BI699308
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|58022417|gb|CX709158.1|CX709158
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|33388305|gb|CA851512.1|CA851512
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTCGAATACGAG                         GTTCACCGCCTCGTCGTNGGNAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|9258866|gb|BE347013.1|BE347013
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
EST: gi|151399436|gb|EV269307.1|EV269307
EST:     AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG                         GTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG
genomic: AATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattc ... aattcctcagGTTCACCGCCTCGTCGTAAACAGAGACCCTAAATACACAAATTTCGTCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAGgtaacaattctacttcttcttcatacacaacaccaccaccttaacctaattggagacataaggttcgtctacgggagaagagaaggggaagagatcgcgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA