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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttcatcattattctttcagattgtgtattcgcctcaatgtctatattctggacagattactgaaaccatttcttttccgcttcctatgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGATCAAACATCAAAAGAGTGCCTCAAACAACTTAACCAG

Basic information

species Glycine max
transcript GLYMA05G32510.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 2
-----ttatttcatcattattctttcagattgtgtattcgcctcaatgtctatattctggacagattactgaaaccatttcttttccgcttcctatgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGATCAAACATCAAAAGAGTGCCTCAAACAACTTAACCAG
     |  |||    |  |||   |    ||   |  |  |    |||  ||| |  |    | | | |  |    ||  || |||       ||| |    |||||||  ||| |||||||||||||| ||||||||||||||| | |||||||||   |  || |||||||| ||||  || ||  | |||
gtacttgcttttgaaagcatttactgtattttcatccttacggagatgaatatttcttttctacaatgcatactgaatcgctattcaaaaatgtatttaatgcagTGAAGGTGGCCAAATGTGTGCAATTAAAGAGGTCAAGGTTATTTCTGATGATTCTAACTCGAAAGAGTGTCTCAGGCAGCTACATCAG

upper sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 2
ttatttcatcattattctttcagattgtgtattcgcctcaatgtctatattctggac--agattactgaaaccatttcttttccgcttcctatgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGATCAAACATCAAAAGAGTGCCTCAAACAACTTAACCAG
  ||     || ||       | | | | ||||   ||   | | || ||| |      | | | ||     |  |  | |   | || |      | ||||||| || ||  |||||||||| || ||||||||||||||  | ||||| ||||||||||||||||| || || || ||||| || |||
--ataaaggcaatagaaagaaaaagtttctattatgctagctctttacattgtaactctaaactgcttgtttccatcgtataatgttttcgccaacttacagTGAGAAAGGGAAAATGTGTGCTATTAAAGAGGTCAAGGTCATTTCTGACGATCAAACATCAAAAGAATGTCTGAAGCAACTAAATCAG

upper sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 2
ttatttcatcattattctttcagattgtgtattcgcctcaatgtctat-attctggacagattactgaaaccatttc--ttttccgcttcctatgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGATCAAACATCAAAAGAGTGCCTCAAACAACTTAACCAG
 |||||||  |      | | | || ||  |   | ||  || | | |   | |   ||| ||| |  |    | |   | ||  |  | | || ||| |||||||||| || ||||||||||| |||||||| ||||||||||| || |||||||| ||||||||||| ||||| || ||||| ||||||
ctatttcaaaaac-ccatgttaaatggta-aggagactatatatttgttgctttattcagtttattttatttttctaaatgttgtgtatgcaat-tttaacagTGAAAACGGGCAAATGTGTGCGATAAAAGAAGTCAAGGTTGTTTCAGATGATCATACATCAAAAGAATGCCTTAAGCAACTGAACCAG

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|254325845|gb|GR838726.1|GR838726
EST:     AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAG                         TGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGA
genomic: AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAGgtaactatta ... tgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGA
EST: gi|14205575|gb|BG839253.1|BG839253
EST:     AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCA-TAG                         TGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGA
genomic: AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAGgtaactatta ... tgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGA
EST: gi|22521983|gb|BU080794.1|BU080794
EST:     AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAG                         TGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGA
genomic: AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAGgtaactatta ... tgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGA
EST: gi|208248814|gb|GE046313.1|GE046313
EST:     AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAG                         TGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGA
genomic: AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAGgtaactatta ... tgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGA
EST: gi|16348767|gb|BI974362.1|BI974362
EST:     AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAG                         TGAAAATGGACAAATGTGTGCA
genomic: AAGCTTCTAGGACGGGGAACATTTGGGCATGTATATCTGGGATTCAATAGgtaactatta ... tgtttgacagTGAAAATGGACAAATGTGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattctggacagattactgaaaccatttcttttccgcttcctatgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGATCAAACATCAAAAGAGTGCCTCAAACAACTTAACCAG
                           tttcttttccgcttcc  CT-rich tract
                          atttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttcatcattattctttcagattgtgtattcgcctcaatgtctatattctggacagattactgaaaccatttcttttccgcttcctatgtttgacagTGAAAATGGACAAATGTGTGCAATAAAAGAGGTCAAGGTTGTCTCTGATGATCAAACATCAAAAGAGTGCCTCAAACAACTTAACCAG

- - - - - - - - - - - gattgtg
- - - - - - - - - - - - - - - - -cgcctca
- - - - - - - - - - - - - - - - - - - - - - - - attctgg