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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA

Basic information

species Glycine max
transcript GLYMA08G22140.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
                        |    | ||  | |   | | | || || |       || |||  || | |   | | |  ||   ||||  |    |     |||| | ||      ||| |   || ||| ||   ||  | ||| | ||||||||||| || ||| ||||   |||||  ||||| |||||| |||| ||||||||||| |||||||| ||||||||  | ||||| || ||  
-----------------------gtaagttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttt---tttacca-tggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 5
gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
                                                             |   |||  |  | || || |||| |   |   |   |||||  || |     ||| | |     ||||    || ||  |   || ||| | ||||| ||| | ||  |||| ||| | ||  |  | || |  ||| ||||||| |||||||||||||| || |||||||| || ||||||||  || 
------------------------------------------------------------gtaagtttttctgc-attttgttggctctgtagttcaatgatgtaacatctacttgatgtaactataacacaacaa-ttatacc-ttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 14
gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctat---gtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaa---acattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
|||||   | | | |   | |      ||| ||      |||||| ||| |   | |  ||   ||||    ||| |    | |    ||||    | ||    |  |   |   | ||||    | |||   | |  ||  |||  ||  ||| || | ||||| ||| ||||  |||||||  | ||  |  | |  | |||| ||||||| |||||||||||||| || |||||||| || |||||||||||| 
gtgagttctgtcactgtcttaattgcctatgtt----cagttgacctttcagttacatccactattttttgtcctttttaatgtcaaattaagaagaaattatttttctggtcaaattgaaatgtattaatacaaaagtttccttttatc-ttgtagAGGGATGTAGTTTCATCTCATTTAGACGGAGGGGGTTCAGCTGCTGAGGAAGGTGTGGAAGATGCCTTTGAACTGCTTCATGAGATCAATGAACGTGTCC

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 15
gtgag---gattctaaatact-tgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
|||||     ||  | ||| | |      | ||  | ||| || || | | |   ||   ||||| | | ||     ||     |   |  ||  | ||  ||  |   | |   || | | |||     ||| |  |||| || |        | | ||| | ||| | ||  || ||||| | ||     | || |  ||| ||||||||||||||||||||||  | |||||||| || |||||||||||| 
gtgagttaattttcacatattgtagatactgtagatcacagttttttattgtgc-tggttaagca-catattgtattctgcaact---gacaatggtatgccttgtc-tattatttactaacgcaactctaacttgataacatcta--------gAGGGATCTAGTTTCTTCTCATCTAGATGGAGGGGCATCAGTTGGCGAGGAAGGTGTTGAAGATGCCTTTGAATTGCTTCATGAGATAAATGAACGTGTCC

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 14
gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggtta---aatgaatatctgatggcacttactagtgaagcac-agtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
|||||   | | | ||| | |    ||   | |   |  || ||| |||     | |  ||  | |||    | | | | |    |||   |   |  || |  |       | | |  | | || |  | | |  ||  |||  ||  ||| || | ||||| ||| ||||  |||| ||||| ||  |  | |  | |||| ||||||| |||||||||||||| || |||||||| || || ||||||||| 
gtgagttctgtcattaccttattaattgcctatgttca-gtcgacctttctgttacatccactgatttgtgtcttttatgtcaaattaagaagcaatcattttttctggtcaaatggacatgtactaacacaaaagtttccttttatc-ttgtagAGGGATGTAGTTTCATCTCATTTGGATAGAGGGGGTTCAGCTGGTGAGGAAGGTGTGGAAGATGCCTTTGAACTGCTTCATGAGATCAACGAACGTGTCC

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 14
gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
        | |  || ||  |    || ||  |   ||| || ||||    || ||     |  |  |  || ||||    ||||  ||||| ||   |    |||||     |     || | | ||| ||||    |  | | |||||||| ||||| ||| | || || || ||||||||||| || || ||||| ||||||||||| ||||||||||| || || ||||| |  |||||| | || |
-------gtatggatcctcaaattattaatcct---ctttttaactt---gtgtaa-----ttctcctttcctctatagaattggccaaatgcatgatttggagcact-----gcattccaaattgaactttttttaatttaattttgcagCGCGATGTAGTTACTTCTTACTTGGATAGTGGAAGACCAGTGGATGAACAAGGTGTTGAGGATGCCTTTGAACTTCTCCATGAGACAAATGAAAGAGTTA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 14
gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgat-ggcacttactag-tgaagcacagtaaacattttaacttccattg--ttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
                    |    |  || | | | || |   || | | | |       || |||||   ||||      |   ||  ||   || | ||   ||||   | | || |   |||| |||   | |   |    ||  || ||| | || || ||  |||||||||| |||||||| |  ||||| || |||||||||||||| ||||| |||||  | ||||||||| |    || |||||  
------------------gtaagtatcaatatcatatttctatgctctctttaa-------tctttttctgtcctacaccaatttgtatttgctcatgtcattaacactctttgggtggaattcagtcaactcatgattgtgtgctgcctttcagAGGGACGTTGTAACATCATATTTGGATAGTGGCAAGCCTGTGGACGAGCAAGGTGTTGAGGATGCGTTTGAATTACTTCATGAAGTATCGGAGCGTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
                                  ttttaac  putative branch site (score: 2)
                                        cttccatt  CT-rich tract
                            taaacattttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcagCGTGATGTCGTTGCATCATATTTAGATAGTGGAAGCCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG