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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcattgtcaaaagaatctttcttattttcctaccttgcccttctaattacaactttgtcacacctctgcttctaataaatgtaaatgatactcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA

Basic information

species Glycine max
transcript GLYMA15G17070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G17070.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
------------ctcattgtcaaaagaatctttctt-attttcctaccttgcccttctaattacaactttgtcacacctc-tgcttctaataaatgtaaatgatactcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA
             |||   ||| |  | |  | ||  |   |  |     |         |||| | ||  | | ||    || ||   |    || | ||  |    |||||||||||||| ||||||||||||||||||||||| || |||||  | ||||| || || || ||||| ||||| |||||||||||||||||||||||||| |
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA

upper sequence: GLYMA15G17070.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G06430.1 (Arabidopsis thaliana), 3'ss of exon 4
ctcattgtcaaaagaatctttcttattttcctaccttgcccttctaattacaactttgtcacacctctgcttctaataaat-gtaaatgatact---cttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA
             | |||| |  ||   ||| | ||| |  |  |  || |   | |   | ||   ||  |  | |  |  ||| || ||  |   |||||||||||| || |||||||| |||||||| || || || ||||| || ||||| ||||| |  ||||| ||||| || ||||| |||||||||||||||||||
-------------gtatctcttctacactcccagctt-cagtatttttttctgttatcctaaactagtgaatgaacttgacagtatatcatcatttacttgcagATGGTGACAACATTTGGGATGTCTGAAATCGGACCATGGTCGCTAATGGATTCATCGGAGCAAAGCGATGTCATTATGAGGATGATGGCAAGAAACTCAA

upper sequence: GLYMA15G17070.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 3'ss of exon 4
ctcattgtcaaaagaatctttcttattttcctaccttgcccttctaattacaactttgtcacacct--ctgcttctaataaatgtaaatgatactcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGACTCATCAGCTCAAAGTG---ATGTTATCATGAGAATGATGGCAAGAAACTCAA
||   | |   ||  |  || ||||       ||  |  || || |  ||  | || | || |  |  |||  | | |    | |||   || |  ||||||||||| ||||||||||| |||||||| || || || ||||| || |||||| | || ||||| ||||   |||| |||||||||||||||||||| || |   
cttgctcttttaactaa-ttgcttaacaaataacaatttccctc-acctattatttggacaaatttaactgaatttgacgggtttaataaattcgtttgcagATGGTGACCACATTTGGGATGTCTGACATCGGCCCATGGTCGCTTATGGACACCTCGGCTCAGAGTGCTGATGTCATCATGAGAATGATGGCAAGGAATT---

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|6483241|gb|AW202413.1|AW202413
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG                         ATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... actcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
EST: gi|120496670|gb|EH224837.1|EH224837
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG                         ATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... actcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
EST: gi|22928363|gb|BU545502.1|BU545502
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG                         ATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... actcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
EST: gi|209704655|gb|BW675877.1|BW675877
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG                         ATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... actcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
EST: gi|11273951|gb|BF324338.1|BF324338
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG                         ATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... actcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
EST: gi|120496340|gb|EH224507.1|EH224507
EST:     CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG                         ATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
genomic: CAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... actcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
EST: gi|151407651|gb|EV277466.1|EV277466
EST:     GGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG                         ATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC
genomic: GGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... actcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacaactttgtcacacctctgcttctaataaatgtaaatgatactcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA
                         ttctaat  putative branch site (score: 2)
                                            tactctt  putative PPT
                         ttctaataaatgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcattgtcaaaagaatctttcttattttcctaccttgcccttctaattacaactttgtcacacctctgcttctaataaatgtaaatgatactcttgcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCATGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - -aaaagaa
- - - - - - - - - - - - - - -cctacct
- - - - - - - - - - - - - - - - - - - cccttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcaca