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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgatccctttttctcccaatgccttgtgatatacttgtaatctgtgtagctgatatattgtaatatatgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGACATTGAGAAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATA

Basic information

species Glycine max
transcript GLYMA10G12350.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacatgatccctttttctcccaatgccttgtg---atatacttgtaatctgtgtagctgatatattgtaatatat-gct------aaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGACATTGAGAAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATA
|||   ||  | |||  ||    || |||| |    || | ||| |  |   |  |     | | || |  | | | |||      | ||||||||  |||||||||||||| || ||||| |||||||| ||||| |||||    ||||| || || ||| |||| || | ||| ||||  || ||||| |
gtagcagaaac-tttcactagtgataccttttacacatctgcttctgctgcttacactaactttttttttttgtgttgctgcttatatatagGTCAACGAAGCTGATATTGAAGAGTTTGAGGCAAACTACAGGGGATCTGAGTCAGAGAAGAAAGACTTGCTTGAGCTTTTCAACAAGTTTAAGGGTAAAA

upper sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 4
---------------------gtacatgatccctttttctcccaatgccttgtgatatacttgtaatctgtgtagctgatatattgtaatatatgcta--aatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGACATTGAGAAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATA
                      |  |  ||  ||  || || |     | |   || || ||  |  |||   || ||| || |    |  |    |   |  |||| ||||| || |||||||| || |||||||||||||| || || |||||    ||||| |||||||||||||| |||||||| |||||||| |||||||
gtcatatcattttgccttattatggaaaatttctgatt-tcacgtaatcctcctatttattttcagactggaaagatgacatgtgaacacttgcattggtagcagGTTACTGAGGCAGATATTGAAGAGTTTGAAGCAAACTACAGAGGATCTGATTCAGAGAAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATA
















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|207792619|gb|GD767381.1|GD767381
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|151412912|gb|EV282724.1|EV282724
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|151396151|gb|EV266028.1|EV266028
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|41145363|gb|CK605574.1|CK605574
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|193395879|gb|FK364448.1|FK364448
EST:     GGGATGTTGTTCTGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGG
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGG
EST: gi|298194691|gb|HO043163.1|HO043163
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|192323158|gb|FK017384.1|FK017384
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|151402844|gb|EV272657.1|EV272657
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|193556711|gb|FK511920.1|FK511920
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAG
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAG
EST: gi|207787948|gb|GD762544.1|GD762544
EST:     GGATGTTGTTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGATGTTG-TTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|151407863|gb|EV277678.1|EV277678
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|193479469|gb|FK444254.1|FK444254
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGAAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|208130358|gb|GD928131.1|GD928131
EST:     AATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTTACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: AATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
EST: gi|16346108|gb|BI971703.1|BI971703
EST:     GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAG                         GTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC
genomic: GGGATGTTGTTCAGAATCTTAAAGAATATTTCAGAGCAATGTACAAGAAGgtacatgatc ... tgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgatatacttgtaatctgtgtagctgatatattgtaatatatgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGACATTGAGAAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATA
                         agctgat  putative branch site (score: 4)
                              atatattgtaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgatccctttttctcccaatgccttgtgatatacttgtaatctgtgtagctgatatattgtaatatatgctaaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGACATTGAGAAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT