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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatctctttccttttctcttatagcttctatctaaagtgaaaatttttaaaaattttgtcttaactgttgatccatgctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG

Basic information

species Glycine max
transcript GLYMA10G33960.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 4
-------------------------------gtatgtatct---ctttccttttctcttatagcttctatctaaagtgaaaattt------ttaaaaattttgtcttaactgttgatccatgct------atgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG
                                 |||| |      ||| ||    |   || | || |   |          |||      ||   ||||   ||| ||   | || |||||||      || || ||| ||||||||| ||||||||||| || |||||||| || |||||||| || || ||| | || |||||||| ||||| |||||||||||||||||||| |
gtacgcagcatctttttgtgtaacatattcgtcatgttttcaagattttctggcttgcaatggattttcgttgtttccctgttttcttctgtttccaattgcatctgaatc-tagacccatgcttttcttatctgcagAGCTTGCAAGACGAGATGATGGATCTTATGGATGTGAGCAATGAAATACAGGAAACTCTCGGAAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAG

upper sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092468_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------gtatgtatctctttccttttctcttatagctt-ctatctaaagtgaaaatttttaaaaattttgtcttaactgttgatccatgctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG
                                                       | ||  ||  ||| | |   |  ||| |  ||  |   ||   |     ||  |  |  ||   ||| |||   |    | |   ||   ||||   ||||||||||||||||||| || |||||||| || | |||||| ||||| ||| | || |||||||| || || || |||||||| || ||||| |
gtatgttattaagcattctcccatctttactctcaccagattcctcgcgctttcagcattgatgccttacatg--catttacactttgttgcttattttcctttttgattgatgttgcatctgaacatatacctcctatgatccatagAGTATGCAAGATGAGATGATGGATCTTATGGATGTGAGCACTGAAATACAAGAAACTCTTGGCAGAAGCTACAACGTCCCAGATGACATCGATGAGGAAG

upper sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G10640.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtatctc--tttccttttctcttatagcttctatctaaagtgaaaatttttaaaaat-tttgtcttaactgttgatccatgctat-----gtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG
||| ||   |   || | |     | | | | || |||||    | ||  ||||      | ||||  ||  ||| |  | |   ||||     ||  |||| || ||||| ||||||||||| || |||||||| |||  ||||||||||||  |  | ||||| ||||| ||| | ||||||| | ||||||||||||
gtacgttgttaagttacttaacaacatcttggttttatcttgtttcaagcttttctctggtatttgatttgcctgatactacgatctattgatggtacagAATTTACAAGACGAGATGATGGATCTGATGGATGTTAGTTCTGAAATTCAAGAATCACTTGGTAGGAGCTACAATATTCCTGATGGCCTTGACGAGGATG

upper sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtatctctttccttttctcttatagcttctatctaaagtgaaaatttttaaaaattttgtcttaactgttgatccatgctatgt-gtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG
    |||| ||||   | || |     ||||||| |     ||     |  |  | | | || |  | |    | ||   |  |||     |||| ||||||||||| ||||||||| | |||||||  |||  |||||||||||||||  | ||||| ||||| ||||| ||||||||||||||||| ||||
----gtatgtcttggttcttattca--agcttctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttgtataccacagAATTTGCAAGATGATATGATGGACTTAATGGATGAGAGTTCTGAAATTCAAGAGACACTTGGTAGGAGCTACAATGTTCCTGATGACATTGACGAAGATG

upper sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtatctctttccttttctcttatagcttctatctaaagtgaaaatttttaaaaattttgtcttaactgttgatccatgctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG
|| |||||  |||| |     |  ||| || ||   |||     |     | |  |        || |||   ||||   |  | | |  ||| | |||||||||||||||||||||| |||||||||||    |||||||||||  |  | || ||||| || |||||||| ||||||||||| |||||||
gtctgtattgctttaccgaggttctat-gcatcatgctagctatatttcatctggaccgccaaactgaacaactgattgtttttgttttcagAGCATGCAAGATGAGATGATGGACCTGATGGATGTAAGCTCAGAAATTCAAGAATCCCTTGGCAGAAGTTACAATGTGCCAGATGACATTGATGAGGATG

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|151406319|gb|EV276134.1|EV276134
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtatct ... ctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
EST: gi|208119277|gb|GD916552.1|GD916552
EST:     CAAGGAGTTGGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
genomic: CAAGGAGTT-GAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtatct ... ctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
EST: gi|192308429|gb|FK000925.1|FK000925
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtatct ... ctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
EST: gi|208168350|gb|GD966870.1|GD966870
EST:     CTAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
genomic: C-AAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtatct ... ctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
EST: gi|208156779|gb|GD957285.1|GD957285
EST:     GATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
genomic: GATCCAAGACATTGATgtatgtatct ... ctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
EST: gi|151406062|gb|EV275877.1|EV275877
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtatct ... ctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaagtgaaaatttttaaaaattttgtcttaactgttgatccatgctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG
       aaaatttttaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatctctttccttttctcttatagcttctatctaaagtgaaaatttttaaaaattttgtcttaactgttgatccatgctatgtgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAAGAGACTTTGGGTAGAAGCTATAATGTGCCTGATGACATTGACGAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG