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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttaaccctttacttttagttatatttgcatctgcacattgatcatgttatttaatgctcggttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAACAAGCTTGCAAAACATCTTCGCAATATTGATTCTCTTGTAATAGCCAAGA

Basic information

species Glycine max
transcript GLYMA13G40130.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G60640.2 (Arabidopsis thaliana), 3'ss of exon 9
-----------gtaaaatttaaccctttact--tttagttatatttgcatctgcacattgatcatgttatttaatgctcggttgaa--tcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAACAAGCTTGCAAAACATCTTCGCAATATTGATTCTCTTGTAATAGCCAAGA
             |||||    |  |  |||  | | | | || |  | ||| | ||         |  |||  |  |      ||  |||| | || || || |||||||||||||||||| | || |||||||| || ||||| ||||| || ||| | || | |||||||||||| || ||| ||||||
gtaatattgtataaaaatccgtcaataaactgatatggatttactcacgtcttctcacctcagcaatactttgttcttaaaacaaaactcagGTCTACGCACCATGGTGTGGCCATTGCCAAGCCCTTGAGCCAATGTATAACAAACTTGCCAAGCATTTACGAAGTATTGATTCTCTCGTCATAACCAAGA

upper sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0004g02890.t01 (Vitis vinifera), 3'ss of exon 9
-----------------gtaa--aatttaaccctttacttttagtt----atatttgcatctgcacattgatcatgtta--tttaatgctcggttgaat--cagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAACAAGCTTGCAAAACATCTTCGCAATATTGATTCTCTTGTAATAGCCAAGA
                 ||||  | | |   | |  |  | || ||    || |     |||| || || ||     ||  | | ||    | ||| |   ||||| ||||| || |||||||| ||||||||| | || ||||||| ||| ||||||||||| |||||||| |     ||||| |||||||| |||||||| |
gtatcatttcattcctagtaataagtgtgtgcttccatctataattctccatctcaatttctgtacttttatgggaataattctgatatgtgcttggaatacagATCTATGCACCATGGTGTGGTCATTGCCAAGCTCTTGAGCCAACATATAACAAGCTTGCCAAACATCTACATGGCATTGAGTCTCTTGTTATAGCCAAAA

upper sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ24976 (Selaginella moellendorffii), 3'ss of exon 9
gtaaaatttaaccctttacttttagttatatttgcatctgcacattgatcatgttatttaatgctcggttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAACAAGCTTGCAAAACATCTTCGCAATATTGATTCTCTTGTAATAGCCAAGA
      |  |   || ||  ||   || ||| |     |  |||||  || | |           |   |    |||||||||||||| ||||| || ||||| ||| |||||||||| || ||||||||||| |||   |  || ||  |  |  | ||||| || || |||||||
-----gtacactgctatatcttagcttgtatat-----tctacattcttcctctcgccacgaatccccctcg--cagATTTATGCTCCGTGGTGCGGGCATTGTCAAGCACTGGAGCCCATCTACAACAAGCTCGCAGCTCGGCTCCGAGAAGTCAAATCTCTGGTGATTGCCAAGA

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|6567366|gb|AW234977.1|AW234977
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|6846143|gb|AW348433.1|AW348433
EST:     ATAATTTTGATGAAATTGNNNNNNNTGAGTCAAAGGATGTTCTCCTCGNG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|254316462|gb|GR827999.1|GR827999
EST:     ATAA-TTTGATGAAATTGTCTGGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|4289796|gb|AI437977.1|AI437977
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|192331238|gb|FK020977.1|FK020977
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCGATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|192331239|gb|FK020978.1|FK020978
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCGATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|21285376|gb|BQ473247.1|BQ473247
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|21285317|gb|BQ473188.1|BQ473188
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|254316461|gb|GR827998.1|GR827998
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|192326874|gb|FK015131.1|FK015131
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|33387977|gb|CA851184.1|CA851184
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
EST: gi|23731199|gb|BU763711.1|BU763711
EST:     ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAG                         ATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC
genomic: ATAATTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTCCTCGAGgtaaaattta ... gttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttatatttgcatctgcacattgatcatgttatttaatgctcggttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAACAAGCTTGCAAAACATCTTCGCAATATTGATTCTCTTGTAATAGCCAAGA
                                 atttaat  putative branch site (score: 4)
                         atcatgttatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatttaaccctttacttttagttatatttgcatctgcacattgatcatgttatttaatgctcggttgaatcagATTTATGCTCCCTGGTGTGGCCATTGCCAATCACTGGAGCCAATATACAACAAGCTTGCAAAACATCTTCGCAATATTGATTCTCTTGTAATAGCCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT