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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcggttccattttccttcgttttctctgcgattaatttaggtttattgattttatttatttgtattggtttgttgttcag

Basic information

species Glycine max
transcript GLYMA12G08760.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g05300.1 (Oryza sativa), 5'ss of exon 1
CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcggttccattttccttcgttttctc--tgcgattaatttaggtttattgattttatttatttgtattggtttgttgttcag
                                         ||||| ||||||||||||||||||||||||||||| ||||| || || || ||||| | |     | || | ||| |   | |||||  |        |  |      | | || |  |  |||     ||   |  |  |||
-----------------------------------------ATGGGCCAGATCCAGTACTCCGAGAAGTACTTCGACGACACCTACGAGTACAGgtagatgag-aatcccctcttcttgaatcttctcgttatctccgttgcaaaaccctagtttctgatccttttggccggcgcggcg--cag

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: AC149818.2_FGT004 (Zea mays), 5'ss of exon 1
CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtac-------acgctcggttccattttccttcgttttctctg-cgattaatttaggtttattgattttatttatttgtattggtttgtt-gttcag
                                         ||||||||||||||||||||||||||||||||||| ||||| || || || |||||        || ||||   |||   ||      |||| | | |  ||   |  | |||         |    |         |||||  |   ||
-----------------------------------------ATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGACGACACCTACGAGTACAGgtaaggacgaaaccctcgccgccacgatctgcacctttccccgtctcttcggtctgctttgggtggcaaaaccctaaacccctttttgtccgcgtag

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G038485_T01 (Zea mays), 5'ss of exon 2
CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcggttccattttccttcgtttt--ctctgcgattaatttaggtttattgat--tttatttatttgtattggtttgttgttcag--------
            ||   ||  | ||  | | ||    ||| ||||  ||||||||||||||||||||||||| ||| ||||| |||||||| ||||| | |       |     | |    | ||  | || | |    |||    | ||||||  ||     |    ||| ||  |    || |         
---------GAAAGTTGATCGAGAAGTCTTGGTA---GAC-ATGGAGCAGATCCAGTACTCCGAGAAGTACTACGACGACACCTATGAATACAGgtagatgtgaaaccctcgccttcacgatcttcacccttccacatcttttccgtcattgatggttggcaaaaccctatcgggatcccctttatccgcgcag

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G038485_T02 (Zea mays), 5'ss of exon 1
------CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcggttccattttccttcgttttc--tctgcgattaatttaggtttattgat--tttatttatttgtattggtttgttgttcag--------
        | ||       |  | || |   |      ||       ||||  ||||||||||||||||||||||||| ||| ||||| |||||||| ||||| | |       |     | |    | |||   || | |    |||    | ||||||  ||     |    ||| ||  |    || |         
GTTTGGGGATTTTCTGTAGGAAAGTTGATCGAGAAGTCTTGGTAGACATGGAGCAGATCCAGTACTCCGAGAAGTACTACGACGACACCTATGAATACAGgtagatgtgaaaccctcgccttcacgatcttcacccttccacatcttttccgtcattgatggttggcaaaaccctatcgggatcccctttatccgcgcag

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G27970.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcggttccattttccttcgttttctctgcgattaatttaggtttattgatttta-tttatttgtattggtttgttgttcag-------
     | |||  |    |           |  |||  || |||||||||||||||||||||||| || || |||||||| ||||  ||||| ||||  |  ||| |||  ||| |||| |  |||   ||   ||   |      | ||  ||| | | || | |  | ||| | || ||          
-----TAAATTTAATAGACGTTTGTTGGGTGATTTAAGAAGATGGGTCAGATCCAGTACTCCGACAAATATTTCGATGATACTTTCGAATACAGgtg-attctcagtttgattctcctcccattttaatggagttctctctcacgttttagtttcagtctaatcgcgt-ggtcttttatttttctctcag

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G27960.1 (Arabidopsis thaliana), 5'ss of exon 1
-------CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcggttccattttccttcgttttctctgcgattaatttaggtttattgattttatttatttgtattggtttgttgttcag
       |    |     ||   |     || | |   |     ||  |||||||||||||| ||||||||||| ||||||||||||||||  ||||| ||||| | ||||  ||| || |  |||| || |  || | |||  || |   | |      || | || | ||| | | | |   | |||
CCTTCTCCTCCATTTCCTGATTAAGGCTTCACATCTCTGAGAGAGA-AATGGGTCAGATCCAATACTCCGAGAAATACTTCGATGACACTTTCGAATACAGgtaaa-gctc--ttcaatctcgcttc-ttcttcctccaatt--ttcactctcac-----ttctctaatcgtaatcgatcg--atacag

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0061g00810.t01 (Vitis vinifera), 5'ss of exon 2
---CAAATTGA--ATCGAGCGAATTCACA--AACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcggttccattttccttcgttttctctgcgattaatttaggtttattgatt--ttatttatttgtattggtttgttgttcag
   | | |||   |||    ||||    |  ||     ||    ||  |||||||||||||||||||| ||||||||||| |||||||| || || || |||||   | |   |   | |||  ||   |||     | |||  ||| ||||  | |     || |||     | | | ||   ||| |||
ACCCTAGTTGTTCATCTGTAGAATCTGAATCAAGAACGGTGAGGGA-AATGGGTCAGATCCAGTACTCTGAGAAGTACTTTGATGACACCTACGAGTACAGgtaatagtttcatagtaatttgattgcattttgtacctatttttttgggttcttgggagaattgtttgaagatgtggatta--tgtacag

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S7_399V6.1 (Physcomitrella patens), 5'ss of exon 2
-----CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACG-ATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgc--tcggttccattttcc--ttcgttttctctgcgattaatttaggtttattgatttta--tttatttgtattggtttgttgttcag--------
     |   ||      |  |   |   |||    ||   |  | | |||  |||||| ||||| || ||||||||||||||||||||||| || || |||| |  ||  |||| ||  ||||    |||  | ||| || | ||  ||  | || | |||  | |   |   |||  |||||    ||   ||        
CTTTCCTGCTTTGGAAAATAGTGGTGGGAAAGAACAGCGCTTAAGGGATGCCTCAGATTCAGTATTCTGAGAAGTACTTCGATGACACTTACGAGTACAGgtgcgtgccctcgggtcggtttttgagttccatgtctttgaggtt--ttgggtttcagtgacctaaagctcggttgctttggtgatctgagaagaaccgcga

upper sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S36_271V6.1 (Physcomitrella patens), 5'ss of exon 2
--------CAAATTGAATCGAGC--GAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcgg---ttccattttccttc-gttttctctgcgattaatttaggtttattgattttatttatttgtattggtttgttgttcag---------
        |  |     | ||||  ||| | | | |  || | |    || |||   |||||||||||||| |||||||||||||| || || || || ||| ||| |  |   ||   ||   |  |  ||  | |     || ||     || |||||  || | |        ||      |  || |   |          
GAAGTGTGCTCACACCCTTGAGCCAGAAGTGAGAGAAACTCGGT----ACAATGCCCCAGATCCAGTACTCGGAGAAGTACTTCGACGATACCTACGAGTATCGgtgcgtgtcggggggttgtgtggtgattgaggtcgagttgtgacggtgttgggttt-ctggtctcgggagcctgagggattgggtcgagaaatatgtgtgg

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|57574369|gb|CX547344.1|CX547344
EST:     GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
genomic: GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
EST: gi|192324097|gb|FK019388.1|FK019388
EST:     GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
genomic: GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
EST: gi|302141347|gb|HO212223.1|HO212223
EST:     AGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGGATCGTCT
genomic: AGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
EST: gi|192301123|gb|FG988948.1|FG988948
EST:     AGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
genomic: AGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
EST: gi|192317957|gb|FK010235.1|FK010235
EST:     GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
genomic: GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
EST: gi|151412005|gb|EV281816.1|EV281816
EST:     GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
genomic: GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
EST: gi|57574181|gb|CX547156.1|CX547156
EST:     GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
genomic: GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
EST: gi|31469530|gb|CD411558.1|CD411558
EST:     AGAAGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
genomic: AGAAGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
EST: gi|151399098|gb|EV268969.1|EV268969
EST:     GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAG                         ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT
genomic: GGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctc ... tgttgttcagACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAATTGAATCGAGCGAATTCACAAACCCTAGTTTTCGACGATGGGTCAGATCCAGTACTCCGAGAAGTACTTCGATGACACTTATGAATATAGgtacacgctcggttccattttccttcgttttctctgcgattaatttaggtttattgattttatttatttgtattggtttgttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT