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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctccctggtttgcttatattttatttgagtcaagtgcaattcaacacctcagaaaatggaagaaatgattcaaatttgggttccctgtttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAAAACATCTTCAAGCAGAAACCCCCACAGTCTGATGCATCAAGTAGTGGCT

Basic information

species Glycine max
transcript GLYMA13G09260.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G09260.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g15090.t01 (Vitis vinifera), 3'ss of exon 6
ccctccctggtttgcttatatttta--tttgagtcaagtgcaattcaac-acctcagaaaatggaag---aaatgattcaaatttg--ggttccctgtttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAAAACATCTTCAAGCAGAAACCCCCACAGTCTGATGCATCAAGTAGTGGCT
         ||| || | | |  ||  ||| | |    |   ||  |   | ||    ||    ||    | ||| |  |||| |   |||    |||| |||||||||||||||| |||||||| ||  |||||||||| ||    || || | ||| |||||||| ||||||||||| ||  | |||||||| ||||  ||||| |
--------agttggcgtgtgtcataaatttaaatgtgttattatgtagttatctggtgaagcataactgtatatggtaaaaatctaatggtattttgttgatctgcagATTTTGGAAACACCAAGTCTTCTGGCTGAGGGTTCAAGTGGCGTAAGAAAGAACATCTTTAAGCAGAAACCTCCGGAATCTGATGCGTCAACCAGTGGGT
















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|163928959|gb|EH038663.1|EH038663
EST:     CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAG                         ATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGNNNNNN
genomic: CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAGgtacgcatac ... ttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAA
EST: gi|207822874|gb|GD793675.1|GD793675
EST:     CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAG                         ATTTTGGAGACACCAAGCCTCTTGGCTGAGG
genomic: CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAGgtacgcatac ... ttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGG
EST: gi|208129341|gb|GD932309.1|GD932309
EST:     CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAG                         ATTTTGGAGACACCAAGCCTCTTGGCTGAGG
genomic: CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAGgtacgcatac ... ttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGG
EST: gi|151394671|gb|EV264542.1|EV264542
EST:     CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAG                         ATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGNNNNNN
genomic: CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAGgtacgcatac ... ttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAA
EST: gi|254322261|gb|GR837675.1|GR837675
EST:     CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAG                         ATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGNNNNNN
genomic: CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAGgtacgcatac ... ttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAA
EST: gi|6666345|gb|AW277804.1|AW277804
EST:     CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAG                         ATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGNNNNNN
genomic: CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAGgtacgcatac ... ttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAA
EST: gi|208037279|gb|GD836608.1|GD836608
EST:     CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGACGAGCTTGTGATGACG                         ATTTTGGAGAC
genomic: CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAGgtacgcatac ... ttatctgcagATTTTGGAGAC
EST: gi|10254668|gb|BE822434.1|BE822434
EST:     CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAG                         ATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGNNNNNN
genomic: CAAAAACCAGAGTCAATGTTGCACAGTGTTTTGATGAGCTTGTGATGAAGgtacgcatac ... ttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacctcagaaaatggaagaaatgattcaaatttgggttccctgtttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAAAACATCTTCAAGCAGAAACCCCCACAGTCTGATGCATCAAGTAGTGGCT
                                     ttccctgtttatct  CT-rich tract
                   aaatgattcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctccctggtttgcttatattttatttgagtcaagtgcaattcaacacctcagaaaatggaagaaatgattcaaatttgggttccctgtttatctgcagATTTTGGAGACACCAAGCCTCTTGGCTGAGGGCTCGTCCGGTGTGAAAAAAAACATCTTCAAGCAGAAACCCCCACAGTCTGATGCATCAAGTAGTGGCT

ccctccc
- - - - - - tgcttat
- - - - - - - - - - - - - - - - caagtgc
- - - - - - - - - - - - - - - - - - - - - -caacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaagaaa