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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttaatatgaaatacaaatacctacaactttatctgccttttggttcattaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA

Basic information

species Glycine max
transcript GLYMA06G05580.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 4
atgtttaatatgaaata--caaatacctacaactttatctgccttttggttca-ttaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA
  ||||||| |    ||  |    |   |||  ||  | | |  | || |  | | |||   | | ||  |  | | ||| ||||||| |          ||||| || || || || ||||| || ||  | ||| | |||||||| ||||||||||| ||||||||||| |||||||| || |||||||||||||| ||||
--gtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataatttga-tttctctgt----------cagATATACGACATCTTCCAGCTTCTTCCTTCCAAGGTTCAGGTTGGTGTTTTCTCTGCTACAATGCCTCCCGAAGCCCTTGAGATCACAAGGAAGTTCATGA

upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 4
atgtttaatatgaaatacaaatacctacaactttatctgccttttggttcattaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA
  ||||  |||    | ||||    |   | | || |  |  | |||||   |  ||| |   |  ||   || ||  ||  | | |    |  || ||||||||||| || || ||||| || ||||| ||||| |||||||| || |||||||| ||||||||||| |||||  |||| |||||||| || || ||||
--gtttgttatcttcttcaaag---tttgaatctacc--ctctgtggttatctctgatat---tgacttggttttgtgttgttttctggtgaatttgcagATCTATGACATATTCCAGCTTCTCCCACCAAAGATTCAGGTTGGAGTGTTCTCTGCGACAATGCCTCCGGAAGCTTTGGAGATCACAAGAAAATTCATGA

upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 4
atgtttaatatgaaatacaaatacctacaactttatctgccttttggttcattaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA
              || ||||||  |   | | | ||       |   || |||   | || |||     | ||| |||     || |      || ||||||||||| || || ||||| || ||||| |||||||| ||||| || ||||| || |||||||| || ||||| || || |||||||||||||| ||||
------------gtatgcaaatatttctcagtgtttcaattccatt-ctcgttatagtttaactt----gaatctcactggt--ttctgggttttttcagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTCTCCGCAACAATGCCACCAGAAGCTCTTGAGATCACAAGGAAGTTCATGA

upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 3'ss of exon 3
---atgtttaatatgaaatacaaatacctacaactttatctgccttttggttcattaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA
   |  | |    |   |  ||  |   |     |||     | ||   || ||||   |||    |||||   |  |||   |    |||  ||  |  ||||||||||||||||| ||| |||||||| | ||||| ||||||||||| ||||||||||| ||||| ||||| ||||| || ||||||||||| || ||||
tttagctatgtggttgcaagcattttgttgtgggttttctgactttcatgtgcattctaatgctgatttcttg-tcttgatactgaaattt--catttggcagATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTCTCTGCCACGATGCCACCTGAGGCCCTTGAGATCACAAGGAAATTCATGA

upper sequence: GLYMA06G05580.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 3
atgtttaatatgaaatacaaatacctacaactttatctgccttttggt--tcattaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA
 |||| | |         |  |  |      || ||  |  | |||||     ||| | || |     | |  | ||  |  |    |  |  || | | |||| || || || |||||||||||||| |  ||| | || || || ||||||||||| || ||||||||||||||||| || |||||||||||||| ||||
gtgttgagtggtctgagtatgtcgcactgttttgataggggtgttggtgactgttacggtgaaaagg-ccgcttacttgcagtgatgtccaatacgtgc-agATTTACGACATCTTTCAGCTGCTGCCCCAGAAGCTTCAAGTGGGTGTTTTCTCTGCTACCATGCCTCCTGAAGCCCTCGAGATCACAAGGAAGTTCATGA

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|16995721|gb|BM085093.1|BM085093
EST:     TTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAG                         ATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTC
genomic: TTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcat ... caccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTC
EST: gi|10846343|gb|BF069261.1|BF069261
EST:     TTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAG                         ATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTC
genomic: TTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcat ... caccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcattaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA
                          ttctgac  putative branch site (score: 2)
                          ttctgactttctcttt  CT-rich tract
     attaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtttaatatgaaatacaaatacctacaactttatctgccttttggttcattaagatgtatctttctgaattctgactttctcttttaccaccttccagATCTATGATATTTTTCAGCTGCTGCCACCTAAGATCCAGGTTGGGGTTTTCTCTGCCACAATGCCTCCTGAAGCCCTGGAAATCACAAGGAAGTTTATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - -gaaatac
- - - - - - - - - - - acctaca
- - - - - - - - - - - - - - - - - - ctgcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttctg