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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatacctttgttgatgttgcacaaactttctttggaattattttgtcacactggtattttatctcttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGTGGTAGTGGTTCTC

Basic information

species Glycine max
transcript GLYMA16G21340.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 10
--gtataatacctttgttgatgttgcacaaactttctttggaattattttgtcac-----actggtattttatctcttggttgt-agGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGTG-GTAGTGGTTCTC
   |   | | ||| |  |   | |   | | |      |    | || | |||       ||| ||   || |  |   || | |||| || ||||| |||||||| ||||| ||||| ||||||||||| ||||| ||  | ||||| |||||| | || | |  | ||| |   |          
gtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGGTAATAGTGTTACATCACAAAATG-

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtataa-tacctttgttgatgttgcacaaactttctttggaattattt-tgtcacactggtattttatctcttgg----ttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGT---GGTAGTGGTTCTC
|| |||  | |  | ||  ||   ||  |  ||     | ||||  || ||  | | |    ||   |  ||||     ||||||||||||||||||||||| ||| | || ||||| ||||||||||| ||| ||||||| || || |||||  |||| |||||   | |    | || |||     
gtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttgggtaacttgtatgtttgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG---

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------gtataatacctttgttgatgttgcacaaactttctttg------gaattattttgtcacactggtattttatctcttggt-tgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGTGGTAGTGGTTCTC
                                                || | |  |  || ||  | ||    |  | || ||||       ||  ||| |       | |  || |||  | |  | || ||||||||||||||||||| ||||||||||| || ||||||||||| ||| ||||||||||||| |||||| | || |||||| ||||   ||    |    
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 13
----gtataatacctttgt-tgatgttgcacaaactttctttggaattattttgtcacactggtattttatct--cttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGT--GGTAGTGGTTCTC
     | |  |||||   | |    ||| ||   |          |||||||||  | | |  | |||  | |  ||||   | |||| ||||| ||||| ||||| |||||||||||||| |||||||| ||| |||| || || || | |   | |     | ||  |||   ||||     |   
gttattttcgtacctagatcttgctttgtacttgcaaatccctatattattttgg-agatttatttttggtttgtcttgtgagcagGGGGAAGACATTTGCGTAGCACTTCAGACACACATTAATGATGTTATGTTGCGGCGATACTCCAGAAACAAAAATATTCCTAATGGGCAGGTATCAAATG--

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 11
gtataatacctttgttgatgttgcacaaactttctttggaattattttgtcacactggtattttatctcttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGTGGTA-GTGGTTCTC
                              | ||||||    | ||  ||   | |  |  | ||  | |  || | |||| |||||||| || || ||||| |||||||||||||| ||||| ||||||||  | ||||| | | |  | || | ||||   || |  |       |  
-----------------------------gtgtctttgtggct-ttccgt-gtagttcttctctaaatttctgtcgcagGGCGAAGAAATATGCGTGGCTCTCCAGACACACATAAACGATGTGATGCTGCGGAGATATTCAAGAACGCGTTCTGTTGCTAACGGAGCCATACAAAGCA-

upper sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 11
gtataatacctttgttgatgttgcacaaactttctttggaattattttgtcacactggtattttatctcttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGTGGTA-GTGGTTCTC
                              | | ||||    | ||  ||   | |  |  | ||  | |  || | |||| |||||||| || || ||||| |||||||||||||| ||||| ||||||||  | ||||| | | |  | || | ||||   || |  |       |  
-----------------------------gtgtttttgtggct-ttccgt-gtagttcttctctaaatttctgtcgcagGGCGAAGAAATATGCGTGGCTCTCCAGACACACATAAACGATGTGATGCTGCGGAGATATTCAAGAACGCGTTCTGTTGCTAACGGCGCCATACAAAGCA-

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|208309605|gb|GE108059.1|GE108059
EST:     AAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAG                         GGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTG
genomic: AAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataatacc ... ttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTG
EST: gi|208212811|gb|GE010470.1|GE010470
EST:     AAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAG                         GGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTG
genomic: AAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataatacc ... ttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTG
EST: gi|208068710|gb|GD865776.1|GD865776
EST:     AAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAG                         GGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTA
genomic: AAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataatacc ... ttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCT-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaactttctttggaattattttgtcacactggtattttatctcttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGTGGTAGTGGTTCTC
                                    ttttatctctt  CT-rich tract
          tttggaattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatacctttgttgatgttgcacaaactttctttggaattattttgtcacactggtattttatctcttggttgtagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGTCGCTATTCGAAAGCAAGATCAGCTGCTGGTGGTGGTAGTGGTTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG