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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacctttgattgctattttattagtattttagctgttatcttgcaaaaggtcttgtaagaattttccatcaaacaagGCTAGGATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA

Basic information

species Glycine max
transcript GLYMA10G33310.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os12g16650.1 (Oryza sativa), 3'ss of exon 17
------------------------------------------------------------------------------------------------gtaagtacctttgattgctattttattagtattttagctgttatcttgcaaaaggtcttgtaagaattttccatcaaacaagGCTAGGATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
                                                                                                | |  |      ||   || | ||||   |||    | | | || || |   |  |||| ||    |   |  | |   |||||||   | |   ||    ||||| |||||||||||||  |||| ||||| ||||| || || ||||| || || ||||| ||||||||||| || ||  
gtgataattctatcatatagtagtttttgtgtttccacctatctctctctcaccacataatgagagagaacatatgtcttgatcgatatttactatgaagatgaacccgacc-ctttcttatctatatacatggtctgatgttccttcaa-tcttttacatgtccact-taatgaaagGCTAAAGTGGGACAGGATGATGAAGTTCTTGAGATTGGTAGTGGTTGGGGCAGTTTGGCTATGGAAGTGGTGAAGCAAACTGGCTGCAAATATACAGGAG

upper sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23480.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtacctttgattgctattttattagtatttta-----gctgttatcttgcaaaaggtctt--gtaag-aattttccatcaaacaagGCTAGGATAGATAAGA--CACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
|||||  |  | |      ||||| |   | ||| |      |   | | ||      | | ||  || |  ||  ||     |    |||| |||||| | ||||  || ||||  || | ||||| ||||| |||||||||| ||||||||| |||||||| |||  ||| || ||||||||||||||  
gtaagatctataggagatcattttctatatttttaacaagaaccactgttttttctttgttttttagtgatcaaaatttggaaatttcagGCGAGGATAAAGAAGAACCATATGAGGTTTTAGAGATAGGATGCGGATGGGGAACTTTAGCCATAGAAGTTGTGAAAAGAACTGGATGCAAATACACTGG--

upper sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaa-gtacctttgattgctattttattagtattttagctgttatcttgcaaaaggtcttgtaagaattttccatcaaacaagGCTAGGATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
|||| | |  ||       ||    |  |   | |    | ||||||         |     ||||        |||     ||| || ||||| |||   || ||  || | ||||| |||||||||||||||| ||| ||||| |||||||| | |  ||| || ||||||||||| || |
gtaaagcattttcttgatttagaacaacaacttgtggttttttatctcttcttgaataaccgaagagggacatttca-----gGCGAGAATAGAGAAGGACCACGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGGA

upper sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23470.1 (Arabidopsis thaliana), 3'ss of exon 8
---------gtaagt-acctttgattgctattttattagtattttag----ctgttatcttgcaaaaggtcttgtaagaattttccatcaaaca----agGCTAGGATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
           | |  || |||  ||| | | | |  || | |  ||    |   ||| ||  |   | |||| |||  ||      |   | |    |||| |||||||| ||||  |||||  |  | ||||| ||||| |||||||||| ||| ||||| |||||||| |||  ||| || |||||||||||||| |
gtaaggtctacaggagacattttcttgatttataacaagaagtcaagagtacacgtattttttatttgttctt-taatgatcaattgtgggaaatttcagGCGAGGATAGAGAAGAACCATGAGGTCTTAGAGATGGGATGCGGATGGGGAACTTTTGCCATAGAAGTTGTGAAAAGAACTGGATGCAAATACACTGGCA

upper sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23480.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtacctttgattgctattttattagtatttta-----gctgttatcttgcaaaaggtctt--gtaag-aattttccatcaaacaagGCTAGGATAGATAAGA--CACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA---
|||||  |  | |      ||||| |   | ||| |      |   | | ||      | | ||  || |  ||  ||     |    |||| |||||| | ||||  || ||||  || | ||||| ||||| |||||||||| ||||||||| |||||||| |||  ||| || ||||||||||||||     
gtaagatctataggagatcattttctatatttttaacaagaaccactgttttttctttgttttttagtgatcaaaatttggaaatttcaggcgagGATAAAGAAGAACCATATGAGGTTTTAGAGATAGGATGCGGATGGGGAACTTTAGCCATAGAAGTTGTGAAAAGAACTGGATGCAAATACACTGGCTTTA

upper sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G23510.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaagtacctttgattgctattttattagtattttagctgttatcttgcaaaaggtcttg--taagaattttccatcaaacaagGCTAGGATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
||||   | |||  ||| | ||  |  |  |  || |   || | |||       ||| |  |||           ||    |||| || ||||| |||   |||||  || | ||||| |||||||||||||||| ||| ||||| |||||||| | |  ||| || ||||||||||| || |
gtaaa-gcattttcttgat-ttagaacaacagctt-gtgatttttttgtttctcttctcgaataaccgaagagggacatttcagGCGAGAATAGAGAAGGACCATGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGCA

upper sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv05s0049g01620.t01 (Vitis vinifera), 3'ss of exon 14
gtaagtacctttgattgctattttattagtattttagctgttatcttgc------aaaaggtcttgtaagaattttccatcaaacaagGCTAGG-----ATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
|| |||   ||      | | |  || | | ||  |    || ||||||      |||  |  ||       ||| ||||| ||| |  |||||     || |||||||  |||||| || | |||||||| ||||| |||||||||||||| |||||||| || |||||||| || || ||||||||||| |
gtgagtcttttctgcaacaactacatgaattttgaattgattttcttgccatgctaaattgattttctgtgttttcccatctaaccaacctagGCAAGAATTGATAAGAAGCATGAAGTTTTAGAGATTGGTTGTGGTTGGGGAAGTTTAGCTATTGAAGTCGTGAAACAAACTGGATGTAAATACACTGGCA

upper sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 18
gtaagtaccttt---gattgctatttta--ttagtattttagctgttatcttgcaaaa--ggtcttgtaagaattttcc-atcaaacaagGCTAGG-----ATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
|| |||   ||     |   ||  || |  || | |||     | ||  | |||||||    | || || |  |||||| ||| ||| |  |||||     || |||||||  |||||| || | |||||||| ||||| |||||||||||||| ||||||||||| |||| ||| || |||||||||||||| |
gtgagtcttttctgcaacaactgcttgaattttgaattgattttcttgccatgcaaaattaattttctatgtgttttcccatctaaccaacctagGTACGAATTGATAAGAAGCATGAAGTTTTAGAGATTGGTTGTGGTTGGGGAAGTTTAGCTATTGAAGTTGTGAAACGAACTGGATGCAAATACACTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtattttagctgttatcttgcaaaaggtcttgtaagaattttccatcaaacaagGCTAGGATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA
                                       ttttccatc  CT-rich tract
                                 taagaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacctttgattgctattttattagtattttagctgttatcttgcaaaaggtcttgtaagaattttccatcaaacaagGCTAGGATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG