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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgcaatattaatcaacattaatttacctatttgtgtcacatttctcttactttgttcttgaaagatgttcaaagctaagaggttgatttaattaattatgtttaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGAGCCTAATGATCAAGAAATCAACTTCTTGTCAGCATGGCACAATTCAGCA

Basic information

species Glycine max
transcript GLYMA01G03940.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G116185_T03 (Zea mays), 3'ss of exon 3
--gtatatgcaatattaatcaacatta-atttacctatttgtgtcacatttct--cttactttgttcttgaaagatgttcaaagctaagaggttgatttaattaattatgtttaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGAGCCTAATGATCAAGAAATCAACTTCTTGTCAGCATGGCACAATTCAGCA
     |||  |  | |||  |||| || | |    || | ||     | | ||     ||  |  | | |   |  || |        |  | ||   |  |    | ||  | || |  |||||||||||| |||||||| || || ||||||||||||||| |   | | ||| |  | || || || |||||| || | ||  | |||  |||  | || 
gtacgtatttagcagtaaataacactacagtggtttactagtagaggactactggtcaaccatcatatcgcgcgcggtcccgttgcctggtgatgtgcttgtgtgctttgcgttattg--cagGTTGATAGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCC

upper sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G136831_T01 (Zea mays), 3'ss of exon 2
gtatatgcaatattaatcaacattaatttacctatttgtgtcacatttctcttactttgttcttgaaagatgtt--caaagctaagaggttgatttaattaattatg-----------tttaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGAGCCTAATGATCAAGAAAT---CAACTTCTTGTCAGCATGGCACAATTCAGCA
|||  ||    | || ||  |||  |     | ||| | |   |  ||  | | | |      | || ||||    |   ||        |  |     |  |  ||           |||  ||  ||||  ||||||| |||||||| ||||| ||||||||||||||| |   ||| |||||  | || || || |    |||| || | ||  | |||  |||  |    
gtaggtggctgactagtccgcatgcacaccacgattagcgagccggttaaccttcctctcctgttaatgatggcgccggggccctcctcctcctcctcctgttcttggtgcggtttcctttcgtgctgcagTCTGATAGGGAAAGTGGCGGCAGACCACAGCCACAAGTGGGTGTTCAAGGAGCCCCAGGAGCACGAGACGAGCAACCTCATCTCCTCCTGGAGCAACCCT---

upper sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G60060.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatatgcaatattaatcaacattaatttacctatttgtgtcacatttctcttactttgttcttgaaagatgttcaaagctaagaggttgatttaattaattatgtttaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGAGCCTAATGATCAAGAAATCAACTTCTTGTCAGCATGGCACAATTCAGCA
  |  ||  | | ||||||   | || | |        | | | | |  |  |   ||  | |   || |   | |    | | |   ||  ||| | |||| |||        ||||||||||||||||||| |||||||||||||| |||||||||||  | ||||| |||||||| ||||| || |||||||| || || ||||| ||||| || 
-gaagtgttaaactaatcattgtcaactaa-------atattataatggttgttaattaatttaataatactctaatgattgaaaaaatg--ttattaaattttgt--------gcagGTTGATAGGAAAAGTAGCTGCAGATCACAGTCACAAGTGGATTTATAAAGAACCTAATGACCAAGAGATTAACTTCTTATCTGCTTGGCATAATTCCGCT

upper sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0026g00350.t01 (Vitis vinifera), 3'ss of exon 3
gtatatgcaatattaatcaacattaatttacctatttgtgtcacatttctcttactttgttcttgaaagatgttcaaagctaagaggttgatttaattaattatgtttaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGAGCCTAATGATCAAGAAATCAACTTCTTGTCAGCATGGCACAATTCAGCA
||| ||  |  ||    | || | | ||| | | | | |      |   |  |  || |  ||   |     |||| |  |||  |    |  |  | |||  |||       | ||| ||||| |||||||||||||||||||| || || |||||| |  ||||||| || ||||| |||||||||||||||||||| ||||||||||| ||||||
gta-ataaagaatcg--ccacttcatttttcttctctatagatgttgattgatcattcgccctgctagtgatttcacaagtaatcgaagaagat--tcaatcctgtc------aacagTTTGATCGGAAAAGTGGCTGCAGATCAGAGTCATAAGTGGGTCTACAAAGAACCAAATGAACAAGAAATCAACTTCTTGTCTGCATGGCACAACTCAGCA

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|207836733|gb|GD807038.1|GD807038
EST:     ACATGAGATTCTATAACTATGGAGAAGG                         GTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
genomic: ACATGAGA-TCTATAACTATGGAGAAGGgtatatgcaa ... aatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
EST: gi|12689978|gb|BG156314.1|BG156314
EST:     CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGG                         GTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
genomic: CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGGgtatatgcaa ... aatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
EST: gi|193468234|gb|FK430491.1|FK430491
EST:     CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGG                         GTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
genomic: CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGGgtatatgcaa ... aatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
EST: gi|298168957|gb|HO020261.1|HO020261
EST:     CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGG                         GTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
genomic: CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGGgtatatgcaa ... aatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
EST: gi|298188019|gb|HO031976.1|HO031976
EST:     CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGG                         GTTGATAGGAAAAGCGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
genomic: CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGGgtatatgcaa ... aatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
EST: gi|16348841|gb|BI974436.1|BI974436
EST:     CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGG                         GTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA
genomic: CCGGAGCTCTTCTTCAAGATGTCACATGAGATCTATAACTATGGAGAAGGgtatatgcaa ... aatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaagatgttcaaagctaagaggttgatttaattaattatgtttaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGAGCCTAATGATCAAGAAATCAACTTCTTGTCAGCATGGCACAATTCAGCA
                     aggttgatttaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgcaatattaatcaacattaatttacctatttgtgtcacatttctcttactttgttcttgaaagatgttcaaagctaagaggttgatttaattaattatgtttaatggagcagGTTGATAGGAAAAGTGGCTGCAGATCACAGCCACAAGTGGATAAACAAAGAGCCTAATGATCAAGAAATCAACTTCTTGTCAGCATGGCACAATTCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA