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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatggttgttcttttttataatgacccctttgccatggaaataatttatagatgctttgatggagaaaatatgatcagtgaattgttgtaattttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG

Basic information

species Glycine max
transcript GLYMA04G05550.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
tatggttgttcttttttataatgacccctttgccatggaaataat--ttatagatgctttgatggagaaaatatgatcagtga----attgttgtaattttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG
        | | ||| ||| ||      |  |    | ||| |||  |  | |  | ||  ||||     ||     |  | |    ||   |    |     |||||||||||||| || || || || || ||  ||||| |||| ||||| ||||| ||||||||||||||||| |||||||| || ||  |||| |||||||
------cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG

upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 1
tatggttgttcttttttataat-gacccctttgccatggaaataatttatagatgctttgatggagaaaatatgatcagtgaattgttgtaattttga-cagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG
                |||  |  |  ||| | | |       | ||| || | | |||| |   |  |||    |  |     ||| |   |||| | || ||||||||||| || || || || || || ||||||||||| ||||||||||| || ||| ||||||| ||||||||||  || ||  |||| ||||   
---------------gtatgtttaagacctctacaaatttttcattttgtaaa-gttttggttttgttaattgcttttggattgtgtcggtgttttaagCACATATCTGGTGAGACTGTTGGAGAGGTAAGAATTGTTTCAGACATGCACGAGCGCAAAGCTACAATGGCTCAAGAAGCTGGGGCTTTCATTGCGCTCC---

upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 3
tatggttgttcttttttataatgacccctttg-ccatggaaataatttatag-atgctt-tgatggagaa--aatatgatcagtgaattgttgtaattttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG
     | ||||  | | ||    |   |||    | ||  |  |  ||  || |||      |||||  |  |||||  |      || | |  |||  ||||||||||||||  |||| || || ||||| || ||||| || || ||||| ||||| || |||| |||||| |||||||||||||| ||| ||||||| ||||
-----tagttccctatgatggaaagtacttcaatcttgtgagcagcttggagcatgtgaacaatggactactaatatattgttaacatgggtaaaatggtgacagATATCTGGCCAAACTGTTGGAGAAGTAAGAATTGTGTCGGACATGCATGAGCGGAAAGCTGAAATGGCTCAAGAAGCTGATGCTTTTATTGCTCTTCCTG

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|58016135|gb|CX702877.1|CX702877
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|308098158|gb|HO761329.1|HO761329
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|151400828|gb|EV270642.1|EV270642
EST:     GACCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|151403620|gb|EV273430.1|EV273430
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|254318543|gb|GR832711.1|GR832711
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|192296477|gb|FG991627.1|FG991627
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|120494056|gb|EH222223.1|EH222223
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|209721044|gb|BW666301.1|BW666301
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|120494245|gb|EH222412.1|EH222412
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
EST: gi|151394491|gb|EV264362.1|EV264362
EST:     GATCATTCCAAAAGCTCTCATGCCTCTCGAG                         ATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG
genomic: GATCATTCCAAAAGCTCTCATGCCTCTCGAGgtatttgtgc ... attttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagatgctttgatggagaaaatatgatcagtgaattgttgtaattttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG
         ctttgat  putative branch site (score: 5)
                                   aattgttgtaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatggttgttcttttttataatgacccctttgccatggaaataatttatagatgctttgatggagaaaatatgatcagtgaattgttgtaattttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT