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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggatgatctttggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgattatgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT

Basic information

species Glycine max
transcript GLYMA02G43930.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
gtaaaggatgatctttggatgttttgtacacaaacatttttgtggaatactgtctca--aattcatgatgattatgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
     |   ||  |||   | | || ||   ||       |    |||| ||| |||  |||  |  |  | | | |  |||        ||||||||  ||| || || || || ||  || |||||||||| ||||||||||| ||||| || ||||| ||||| ||||| ||||| || || || || |
-----gttggacatttatttttgttatatgtaaga-----taataaatagtgtttcatcaatgtacaactactctctcgattc-------agGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 6
gtaaaggatgatctttggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgattatgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                      |    |||  |   || |||||||||  | | |||  |   |||  |||||       ||| |   ||||||||||||| ||||| ||||||||| |||||||||||||||| ||||||||||| || |||||||||||||||||||| ||||| || || |||||||
---------------------gtacaaacatgactgttgttgtggaat--tatttcagttc--tgacaattattaagtgcttgcc---agGGAACTGTTGTGGAGGGCACTATACAGCAGTTATTTGAAGGGCACCATATGAACTACATTGAATGCATCAATGTGGACTACAAATCTACAAGGAAGGAGT

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
--gtaaaggatgatctt-tggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgatt-----atgttaatttt-gtctt---tagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
  ||    |  | | |   || |||| ||  |   ||     || | |  | ||      ||||  |||  | |     || |  ||||  | |||   ||||| || |  || ||||| || ||||| ||  | |||||||| ||||||||||| |||||||||||||||||||| || | ||| || ||| | |||||||
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattg--tgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaaaggatgatctttggatgttttgtacacaaacattttt---gtggaatactgtctcaaattca-tgatgattatgttaattttgtctt-tagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
|||  |    |||| ||   | | |||   |     |||     || |     |   | |  || | || ||   ||  |  | |  | ||  ||||||||| ||| ||||| || || ||| |  | || ||||||||||| |||||||| || || ||||||||||| || |||||||||||  | || ||||
gtatggataaatctctgttagctatgtcttctcggttttcaagagtagctgggtacattatgtttactggtgggaatccttctgtgcttttacagGGAACTGCTGTCGAGGGCACAATCCAGCAACTGTTCGAAGGGCATCACATGAACTACATAGAGTGCATCAATGTTGATTATAAATCAACACGGAAAGAGT

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaggatgatctttggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgatta-tgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                                     |||  ||  ||  | |      |  ||| |   ||     ||  |   ||  || | |||| |||||| || || |||||| || | || ||||| ||||||||||| ||||| ||||||||||||||||||||||| || ||| ||||||| |
------------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ19227 (Selaginella moellendorffii), 3'ss of exon 6
gtaaaggatgatctttggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgattatgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                                |  | ||| ||    |      |||||   ||  | ||  | |  | |   |  | ||||||| | |||||| ||||| || ||  || | ||||| || |||||||||||||| |||||||||||||| || || || ||||| ||  | || ||||
-----------------------------gtgagtacttt-gtacgttga-acttcaaagctattcttatcttct--actcacttctcagGGAACCGCTGTTGAAGGAACGATTCAACAGCTTTTTGAGGGTCATCATATGAACTACATCGAATGCATCAACGTCGATTACAAATCTACGCGGAAAGAGT

upper sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaggatgatctttggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgatta-tgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                                     |||  ||  ||  | |      |  ||| |   ||     ||  |   ||  || | |||| |||||| || || |||||| || | || ||||| || |||||||| ||||| |||||||||||||||||||| || || ||| ||||||| |
------------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAAT

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|254342407|gb|GR858569.1|GR858569
EST:     TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGACAAGATGAAG                         GGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
genomic: TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGATAAGATGAAGgtaaaggatg ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATG
EST: gi|209717383|gb|BW659059.1|BW659059
EST:     GAAAAACTTGAAGACAAGATGAAG                         GGAACTG-TGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATG
genomic: GAAAAACTTGAAGATAAGATGAAGgtaaaggatg ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATG
EST: gi|193646687|gb|FK587448.1|FK587448
EST:     TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGATAAGATGAAG                         GGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATG
genomic: TTCAAGAACTGAACAGAGTCCTCTGTGAAAAACTTGAAGATAAGATGAAGgtaaaggatg ... ttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttgtggaatactgtctcaaattcatgatgattatgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT
                                     tgttaat  putative branch site (score: 3)
                                           ttttgtcttt  CT-rich tract
                                 attatgttaattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaggatgatctttggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgattatgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG