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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcattatgttatactctgagcaatcctttgtcctcctcagtcctctcccccataagacttcttttctacttctcacattagaatcgtaaattggagccttttatttagttaaggtttctgttttcagGGGTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTGGTTTA

Basic information

species Glycine max
transcript GLYMA02G03810.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03810.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G70280.1 (Arabidopsis thaliana), 3'ss of exon 3
gcaagcattatgttatactctgagcaatcctttgtcctcctcagtcctctcccccataagacttcttttctactt---ctcacattagaatcgtaaat----tggagccttttatttagtt---aaggtttctgttttcagGG-GTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTGGTTTA
                                                        ||| |  |  ||  ||  |    ||| |  ||  |  || ||    | |   ||| || | ||||   || |  | || | | | || || ||||| ||||| || || |||  |   ||    || || ||| | ||||| ||||||||||| || || ||||| |||||||||||||| |||||
-------------------------------------------------------gtaatagcttgttcataactgcattcatagaagggttatatatacgtttgcatcttgtactgagttttaaatgcctatgatgtgaagGAGTTACAACTATTGCCGGGGGCAAAACGGTTCGAAATGGAGGGCATGTGGATGGACCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA

upper sequence: GLYMA02G03810.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G23880.1 (Arabidopsis thaliana), 3'ss of exon 4
gcaagcattatgttatactctgagcaatcctttgtcctcctcagtcctctcccccataagacttcttttctacttctcacattagaatc-gtaaattggagccttttatttagttaaggtttctgttttcagGGGTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTGGTTTA
                                           ||  | |   |        |    || | | | |   |  |   |  |  || |   |  ||| |   ||   |    |    |  |||| |||||||| |||||||| || |||  |   || || || || ||| | ||||||||||||||||| || || ||||| |||||||||||||| |||||
-------------------------------------------gtgattttttctgcggttttatggttttgccttttggacaaatgtttggtaagtatcggatttaagaaagaataaaaatgcaatggcagGAGTCACAACCATTGCTGGGGGGAAAATGGTTCGTGGGGGAGGTCATGTGGATGGTCCAAGTGAAGATGCAAAGTTTTCAAATGATTTTGATGTTGTTTA

upper sequence: GLYMA02G03810.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g00330.t01 (Vitis vinifera), 3'ss of exon 4
gcaagcattatgttatactctgagcaatcctttgtcctcctcagtcctctcccccataagacttcttttctacttctcacatta--gaatcgtaaattggagccttttatttagttaaggtttctgttttcagGGGTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTGGTTTA
                                 ||  |   ||||          | |    |  | ||||   |   |||| |  ||||   | ||         | || | ||| |  |||||   | ||||||| ||||||||||| || || ||   | |||| |||||||| ||| | ||||| ||||||||||| || || ||||||||||||||||||||||| ||
---------------------------------gttgtttccagtgtaacagtttagagttgtgatcttctgtgttaaacatcacagaatgagagatcttcaatgctaatattgttgaattttctacctgcagGGGTTACAACAATTGCAGGGGGGAAGCTGGGCCGTGGAGGGGGGCATGTAGATGGGCCAAGTGAAGATGCAAAGTTTTCTAATGATTTTGATGTGGTGTA

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|213595695|gb|DB962467.1|DB962467
EST:     CTATATTGCAGATATAATGAATATGGCAATTAGGAAAATTAGTGATTCAG                         GGGTCACAACAATTGC
genomic: CTATATTGCAGATATAATGAATATGGCAATTAGGAAAATTAGTGATTCAGgcaagcatta ... ctgttttcagGGGTCACAACAATTGC
EST: gi|12773827|gb|BG238754.1|BG238754
EST:     CTATATTGCAGATATAATGAATATGGCAATTAGGAAAATTAGTGATTCAG                         GGGTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTG
genomic: CTATATTGCAGATATAATGAATATGGCAATTAGGAAAATTAGTGATTCAGgcaagcatta ... ctgttttcagGGGTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacattagaatcgtaaattggagccttttatttagttaaggtttctgttttcagGGGTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTGGTTTA
 ttctcac  putative branch site (score: 2)
                                          tttctgttttc  putative PPT
                          ttttatttagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagcattatgttatactctgagcaatcctttgtcctcctcagtcctctcccccataagacttcttttctacttctcacattagaatcgtaaattggagccttttatttagttaaggtttctgttttcagGGGTCACAACAATTGCTGGCGGAAAATGGAGCCGGGGAGGGGGCCATATTGATGGTCCAAGTGAAGAAGCTAAATTTTCTAATGATTTTGATGTGGTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC