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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttttaaacaacatttggtatttggtatgaatatttcgaagctttactactgtgcaggattcaaacattactcattacattttgtcatttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATATTACCGAGGAACGCATGCTGTTATTGTGGTGATAGACAGCAGTGATAGAG

Basic information

species Glycine max
transcript GLYMA20G35430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35430.3 (Glycine max), 3'ss of exon 2
lower sequence: AT3G22950.1 (Arabidopsis thaliana), 3'ss of exon 3
aatgttttaaacaacatttggtatttggtatgaat--atttcgaagctttactactgtgcaggattcaaacattactcattacattttgtcatttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATATTACCGAGGAACGCATGCTGTTATTGTGGTGATAGACAGCAGTGATAGAG
  |   | ||     | ||| |   ||  |  ||   | |      |  |   | |  | |   || |  |  |  | | |    |      ||   || |||| |||||||||||||| ||||| ||  | || || |||||||||||||| || || ||||| |||||||| |||||||| ||||| ||||  || ||||
-cttactaaagtttgaattgtttcctgtcaaaaactaactgttggacactggcaat-cgaatatttgaggcgatgtttacttttatgatatgttgtctttagGTATGGGATCTTGGTGGGCAAGATAGGCTAAGAACTTCATGGGCAACATACTATCGTGGAACACATGCTGTGATTGTGGTTATAGATAGCACAGACAGAG

upper sequence: GLYMA20G35430.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g04460.t01 (Vitis vinifera), 3'ss of exon 1
--aatgttttaaacaacatttggtatttggtatgaatatttcgaagctttactactgtgcaggattcaaacattactcattacattttgtcatttatt-tcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATATTACCGAGGAACGCATGCTGTTATTGTGGTGATAGACAGCAGTGATAGAG
    ||       |   | |||  | |   |      | ||    | | |  | ||||     | | | |  ||  |  |  |||| | |  |||| | |||||| |||||||||||||| ||||||||  ||||||||||||||||||| |||||| ||||||| |||||||||||||| |||||||| |||| ||| ||||
tttctggccagctcgttaattgagactatatgactggacttgtgtgttctggttctgt---aaactgatatgtttattttgccattgtttactttaatatcagGTGTGGGATCTTGGTGGGCAAGAAAGGCTGAGGACATCATGGGCAACTTATTACAGAGGAACTCATGCTGTTATTGTCGTGATAGATAGCACTGACAGAG
















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|298173714|gb|HO017050.1|HO017050
EST:     CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAG                         GTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
genomic: CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAGgtcccttcac ... tttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
EST: gi|37996133|gb|CF807722.1|CF807722
EST:     CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAG                         GTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
genomic: CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAGgtcccttcac ... tttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
EST: gi|192330894|gb|FK021639.1|FK021639
EST:     CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAG                         GTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACACCATGGGCAACATAT
genomic: CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAGgtcccttcac ... tttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
EST: gi|193640440|gb|FK592783.1|FK592783
EST:     CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAG                         GTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
genomic: CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAGgtcccttcac ... tttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
EST: gi|192330253|gb|FK020553.1|FK020553
EST:     CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAG                         GTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
genomic: CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAGgtcccttcac ... tttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
EST: gi|298182623|gb|HO031358.1|HO031358
EST:     CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAG                         GTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
genomic: CTGTTGGTAGCAACGTCGAAGAGCTCGTCTACAAGAATATACGATTTGAGgtcccttcac ... tttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
EST: gi|208289119|gb|GE085412.1|GE085412
EST:     ATACGATTTGAG                         GTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT
genomic: ATACGATTTGAGgtcccttcac ... tttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactactgtgcaggattcaaacattactcattacattttgtcatttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATATTACCGAGGAACGCATGCTGTTATTGTGGTGATAGACAGCAGTGATAGAG
                                             tttatttc  CT-rich tract
                               attacattttgtcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgttttaaacaacatttggtatttggtatgaatatttcgaagctttactactgtgcaggattcaaacattactcattacattttgtcatttatttcagGTCTGGGATCTTGGTGGACAAGAAAGATTGAGGACATCATGGGCAACATATTACCGAGGAACGCATGCTGTTATTGTGGTGATAGACAGCAGTGATAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - -aacaaca
- - - - - - - - - - - - - ggtatga
- - - - - - - - - - - - - - - - - - - - - - - - - -actgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacat