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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatatgctgtatgtcttgcagtttctttaatctaattccatgtgattaaacttatccatgtgactgttgctttgcagGAATGGATAATGGAGCAGTGGGATAAAAACTTTTACATTACTTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG

Basic information

species Glycine max
transcript GLYMA10G44050.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgaaatatgctgtatgtcttgcagtt-tcttta-atcta-attccatgtgattaaacttatccatg--tgactgttgctttg---cagGAATGGATAATGGAGCAGTGGGATAAAAACTTTTACATTACTTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG
  |   | || ||| | |||   |||| | |||| ||||   |||  |     | | |||| |   |  ||| |  || ||||   ||||||||||| |||||||||||||| || ||||  ||||||| ||||||||| ||    | |||||| |||||  | || || ||||||||||
--gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG
















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|58019825|gb|CX706567.1|CX706567
EST:     CTGGTTTTACAGCTCAAGTTTACAAGTTGTCAACCTTTTTCTTGCACAAG                         GAATGGATAATGGAGCAGTGGGATAAAAACTTTTACATTACTTCTATTGCA
genomic: CTGGTTTTACAGCTCAAGTTTACAAGTTGTCAACCTTTTTCTTGCACAAGgtgaaatatg ... tgctttgcagGAATGGATAATGGAGCAGTGGGATAAAAACTTTTACATTACTTCTATTGCA
EST: gi|193640147|gb|FK591832.1|FK591832
EST:     CTGGTTTTACAGCTCAAGTTTACAAGTTGTCAACCTTTTTCTTGCACAAG                         GAATTGGATAATGGAGCAGTGGGATAAAAACTTTT-CATTACTTCTATTGC
genomic: CTGGTTTTACAGCTCAAGTTTACAAGTTGTCAACCTTTTTCTTGCACAAGgtgaaatatg ... tgctttgcagGAAT-GGATAATGGAGCAGTGGGATAAAAACTTTTACATTACTTCTATTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttaatctaattccatgtgattaaacttatccatgtgactgttgctttgcagGAATGGATAATGGAGCAGTGGGATAAAAACTTTTACATTACTTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG
       atctaat  putative branch site (score: 3)
                                            ttgcttt  putative PPT
                      attaaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaatatgctgtatgtcttgcagtttctttaatctaattccatgtgattaaacttatccatgtgactgttgctttgcagGAATGGATAATGGAGCAGTGGGATAAAAACTTTTACATTACTTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC