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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgagtcttgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG

Basic information

species Glycine max
transcript GLYMA02G10060.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 7
------attttgagtct-tgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaatt--ttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
        | || || | ||  |||||   ||| || | | || ||| ||   | | ||    |   |  ||| | |  || || | |    | |  |||  | |  ||| ||||||||||||||| || |||||||||||||||| ||   ||||||| ||||||||  | ||||| ||||| ||||||||||||||||||||||| |
gtataatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaata-atcttcatcttggtgtca-attatgctgactgacagtttattgtttgtttagTTTCCTCCTTGTTACAAAGATATGAGTTTCTGGATCAATGGTGCATTTACAGAAAACAACTTATGTGAGGTTGTCAGAGGAATAGCCGGGGATCTTGTTG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 7
--------------attttgagtcttgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatc--ttgtgagaacattctaattttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
               || ||  ||||   |  ||   | || || |||||     | | | |    || |    ||  || ||   ||   |   || |     |||  | |  ||| |||||||||||||||||| |||||||||||||||| |||  ||||||| || |||||  | ||||| ||||| |||||||| || || |||||||| |
gtataatctctatgtttctgtctcttatttaatgtacacttcatttttttgagaaaatagtcttcatcttggtgtcgattatgctcactgacagtttatcactattgtttgtttagTTTCCTCCTTGTTACAAGGATATGAGTTTCTGGATCAATGATGCATTTACAGAGAACAACTTATGTGAGGTTGTCAGAGGAATTGCTGGTGATCTTGTTG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 7
-----attttgagtcttga-atcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
     |   | | | |  |  ||| |  || |    |  | || || |   |||  ||   ||   | | ||   |  ||   ||        |||   | |||||||||||||||||||||||||||| ||||||||||| ||||| |  || || || || ||| | |||||||||||||||||||| || ||||||||||| |
gtaaaacacttaatgtccatgtctcgtagactaatgaactctagttgaa--gacttatctgtattgtat-gtttaacgatggcaaac--aaaattttgttctgcagTATCCTCCTTGTTACAAGGACATCAGTTTCTGGATAAGTGATTTGTTCACAGAGAATAATTTTTGTGAAGTTGTTAGAGGAATTGCTGGGGATCTTGTTG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 7
attttgagt-cttgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtttgccttt--gcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
   || | | |    | | | |  | |  |||||| ||  |   | ||  |  |  |||  |  | |     |      |   ||    ||| ||||  ||||||||||||||||||||||| ||||||||| ||||| | ||| || || || ||||||||| | ||||| ||||| |||||| | || || ||| ||||  
--attaattacacacaacataataactaaatatttatacct-gttagagccccttgtaaccttctctattggctgctagaaactgactattgtctttttgcagTATCCTCCTTGTTACAAGGGCATGAGTTTTTGGATTAATGAGTCGTTCACAGAAAACAATTTATGTGAGGTTGTAAGAGGAGTTGCTGGAGATTTTGTCC

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 7
attttgagtcttgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtttgccttt--gcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
|||          ||| |  |  | |   ||||| ||  |   | ||  |     |||  |  | |     |      |   ||    ||| ||||  |||||||||||||||||| |||||||||||||| ||||| | ||| ||||| || ||||||||| | ||||| |||||||||||| | || || |||||||| |
attacttacacacaatat-aataactaagtatttatacct-gttagagccccatgtaaccttctctattggctgctagaaactgactattgtctttttgcagTATCCTCCTTGTTATAAGGACATGAGTTTTTGGATTAATGAGTCATTCACAGAAAACAATTTATGTGAGGTTGTTAGAGGAGTTGCTGGAGATCTTGTCG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0027g01480.t01 (Vitis vinifera), 3'ss of exon 2
attttgagt-cttgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtt-tgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
   || | | |    | | | |  | |  |||||| ||  |    |  | || |   |   |||     |     |  ||  |   | |  |   ||||||||||||||||||||||||||||| |||||| ||||| | ||| |  || || ||||||||| | ||||| ||||| |||||| | || || |||||||| |
--attaattacacacaacataataactaaatatttatacctgttagagcccaatgtaaccttctctattggctgctagaaactgactatcgtctttttgcagTATCCTCCTTGTTACAAGGACAAGAGTTTTTGGATTAATGAGTTGTTCACAGAAAACAATTTATGTGATGTTGTAAGAGGAGTTGCTGGAGATCTTGTCG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 8
attttgagt-cttgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtttgccttt--gcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
   || | | |    | | | |  | |  |||||| ||  |   | ||  |  |  |||  |  | |     |      |   ||    | | ||||  ||||||||||||| ||||||||||||||||||| ||||| | ||| || || || ||||||||| | ||||| ||| | |||||| | || || ||        
--attaattacacacaacataataactaaatatttatacct-gttagagccccttgtaaccttctctattggctgctagaaactgactatcgtctttttgcagTATCCTCCTCGTTACAAGGACATGAGTTTTTGGATTAATGAGTCGTTCACAGAAAACAATTTATGTGAGGTTATAAGAGGAGTTGCTGGAGA--------

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ33041 (Selaginella moellendorffii), 3'ss of exon 7
attttgagtcttgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
                                                   | |   | | |  |   |    |||||| ||| || | ||  || |||||||||||| |||||||||||||| || |||||||| |  ||  | || || || ||||| ||||| ||  | || ||||   | || || ||  |||  |
--------------------------------------------------gtacgccata-cgcgctcgcttcttctaactttcgt-tctggtttggcagTATCCTCCCTGTTACAAGGACATAAGCTTCTGGATTACCGATGCTTTCACGGAGAACAACCTGTGCGAGCTCGTCAGAGATGTCGCTGGTGACATTGCCG

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|298182211|gb|HO026386.1|HO026386
EST:     TTTTCCAAGGGTCAGTTGGGAGTCAAATTTAAGCCATTTTCAAAG                         TATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACT
genomic: TTTTCCAAGGGTCAGTTGGGAGTCAAATTTAAGCCATTTTCAAAGgtaacatcta ... gcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACT
EST: gi|11689832|gb|BF597508.1|BF597508
EST:     TTTTCCAAGGGTCAGTTGGGAGTCAAATTTAAGCCATTTTCAAAG                         TATCCTCCTTGTTACAAGGACATGGAGTTTCTGGGATCAGTGAATCATTTA
genomic: TTTTCCAAGGGTCAGTTGGGAGTCAAATTTAAGCCATTTTCAAAGgtaacatcta ... gcctttgcagTATCCTCCTTGTTACAAGGACAT-GAGTTTCT-GGATCAGTGAATCATTTA
EST: gi|19053701|gb|BM732368.1|BM732368
EST:     TTTTCCAAGGGTCAGTTGGGAGTCAAATTTAAGCCATTTTCAAAG                         TATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAATGAATCATTCACC
genomic: TTTTCCAAGGGTCAGTTGGGAGTCAAATTTAAGCCATTTTCAAAGgtaacatcta ... gcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACT
EST: gi|16341914|gb|BI967509.1|BI967509
EST:     CAGTTTTCCAAGGGTCAGTTGGGAGTCAAANNNAAGCCATTTTCAAAG                         TATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACT
genomic: CAGTTTTCCAAGGGTCAGTTGGGAGTCAAATTTAAGCCATTTTCAAAGgtaacatcta ... gcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacacattcctaaaatcttgtgagaacattctaattttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG
                            ttctaat  putative branch site (score: 2)
                                          tttgccttt  putative PPT
                        aacattctaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgagtcttgaatcttgaggaatttatatttttatttcagtggacacattcctaaaatcttgtgagaacattctaattttggtgtttgcctttgcagTATCCTCCTTGTTACAAGGACATGAGTTTCTGGATCAGTGAATCATTTACTGAAAACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - ttcagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttggtg