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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttgtgtaggttctctctctctctctctctctctctctctctctctctctctctcttgtaatgtgcttacctttatttgctgtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGCTGGGAAATATCTTCTTGAGTTACTGAAAATGGACTTGAAGCCCCGAGAT

Basic information

species Glycine max
transcript GLYMA13G27810.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 4
--gtaagttttgtgtaggttctctctctctctctctct---ctctctctctctctctctctct--------ctcttgta--atgtgcttacctttattt----gctgtttctgta-------------gCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGCTGGGAAATATCTTCTTGAGTTACTGAAAATGGACTTGAAGCCCCGAGAT
  | || || | | | | || | |     | | |  ||   | |    | |   | |   ||           |||| |  || |  ||  |||  |||      | || |||||             | || || ||||||||||| || || |||||| | || ||||| ||| | |||||||| |||||||| ||||| || || ||||| |||||||||   || 
gtgcaaattatatcttgatttttttctcatttattactaaacacgaaatatggtttttattcatataaaaatgcttggaggatatatttgacttctttttatcattattgctgtaattatgtaccaaagTTCTTCGACACCTGCTGAAGACCCGCTAAAGCTAGAAGAGTGCCGTCTTGCTGGGAAGTATCTTCTAGAGTTGCTAAAGATGGATTTGAAGCCCAAGGAC

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 4
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 4
--gtaagttttgtgtaggttctctctctc-tctctctctctctctctctctctctctctctctcttgtaatgtgcttacctttat-ttgctgtttc-tgta-----gCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGCTGGGAAATATCTTCTTGAGTTACTGAAAATGGACTTGAAGCCCCGAGAT
  || | || | | |   || |||||||| | | || ||            ||       | |  | | |  |  ||   || |  |||||||||  ||||     | || || |||||||||||||| ||||||||  | || ||||| ||| | |||||||| |||||| | ||||| || || ||||| ||||||||    || 
gtgtgaattgtatctgaattttctctctcatttgtcactaaacagtaaatacttggaggatgtagtttgacttctttttattaaccttgctgttttatgtatcaaagTTCTTCGACACCTGCTGAGGACCCACTAAAACTAGAAGAGTGCCGTCTTGCTGGGAAGTATCTTTTAGAGTTGCTAAAGATGGATTTGAAGCCTAAGGAC

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------------------gtaagtt--ttgtgtaggttctctctctctctctctctctctctctctctctctctctctctcttgtaatgtgcttacctttatttgctgtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGCTGGGAAATATCTTCTTGAGTTACTGAAAATGGACTTGAAGCCCCGAGAT
                                                                       | |||||  ||    | |  |  | |   ||     || |   | |      ||   |        | || |  || | | | | |  | ||| || || || || | ||||||||| || ||| | |||||||| |||||||| ||||| || ||||||||||| || || || || |||||||| || ||||| || 
gtgaggctttcagtcctgaagaccacatttataaatcaacttcaaacgttttcccagatttgtgcttaatagaaagttatttccacaagaacattgtagatcctaaactgtaattgtggaatgcttatttcaaaagttcatatatttgcttct-tcttttttttttgaagTTCTTCAATACCTGCTGAAGACCCATTGAAGTTGGACGAGTGTCGCTTAGCAGGAAAATATCTTCTAGAATTGCTAAAGATGGACTTAAAACCCCGTGAC

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|208217240|gb|GE013900.1|GE013900
EST:     AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAG                         CTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGC
genomic: AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAGgtaagttttg ... gtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGC
EST: gi|193652196|gb|FK597788.1|FK597788
EST:     AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAG                         CTCATCTACACCTG
genomic: AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAGgtaagttttg ... gtttctgtagCTCATCTACACCTG
EST: gi|208226692|gb|GE021889.1|GE021889
EST:     AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAG                         CTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGC
genomic: AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAGgtaagttttg ... gtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGC
EST: gi|207844098|gb|GD817391.1|GD817391
EST:     AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAG                         CTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGC
genomic: AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAGgtaagttttg ... gtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGC
EST: gi|193729945|gb|FK666487.1|FK666487
EST:     AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAG                         CTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAG
genomic: AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAGgtaagttttg ... gtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAG
EST: gi|207737749|gb|GD716437.1|GD716437
EST:     AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAG                         CTCATCTACACCTG
genomic: AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAGgtaagttttg ... gtttctgtagCTCATCTACACCTG
EST: gi|193426010|gb|FK390787.1|FK390787
EST:     AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAG                         CTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGC
genomic: AATACCATGGCTTCTGCAATAGAAGCTATGGGAATGTCTCTTCCCTATAGgtaagttttg ... gtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctctctctctctctcttgtaatgtgcttacctttatttgctgtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGCTGGGAAATATCTTCTTGAGTTACTGAAAATGGACTTGAAGCCCCGAGAT
                           tgcttac  putative branch site (score: 2)
                                           ctgtttct  putative PPT
                                   tttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttgtgtaggttctctctctctctctctctctctctctctctctctctctctctcttgtaatgtgcttacctttatttgctgtttctgtagCTCATCTACACCTGCTGAGGATCCACTAAAGTTGGATGAGTGTCGTTTAGCTGGGAAATATCTTCTTGAGTTACTGAAAATGGACTTGAAGCCCCGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC