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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA

Basic information

species Glycine max
transcript GLYMA06G08480.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
       ||  ||||||    ||   ||||   | |  |||  |  |        ||| ||  || | ||||   |  |||   ||   |||| |||||||||||||| || ||||| ||| | |||||| | ||||||||||| || |||||||| ||  | ||||| || |||||  | |   | | 
------gtttgatatcttgtcatgcatatttttcctttcttttacct--------tagcctatgt-tcctaaccataaaaaacctt--tagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG

upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 8
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
       ||  || |||    |  | | | |  | |   ||   ||        || ||  |  | ||   ||  |  | ||||||   |||| ||||||||||||||||| ||||| ||  |||| ||||| ||||||||||| ||||||||||||||| | ||||||||||||||  | |  || | 
------gttagatctctgctcagttttctca--cttttttttcctagtaccagtctggtaattatttttctaacatc-acactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG

upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 7
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
           | |||| |  | |    |||    |   |  | ||     |   || |    || |||  ||  |   |  ||||   |||| ||||||||||||||||| || || ||  |||| ||||| ||||||||||| || |||||||||||| | |||||| |||||||  | |   | | 
--------gttagatctcttcacacacttta----tttttctagtaccagtctggtaatt---gttttcctaacatcacatttttt---agGGGGAAGCATTGTTTCAGACACACGAGAATCTGGAACACCTAGCAATGATGGAGAGGGTTTTGGGACCTCTACCAGAGGATATGATACGGAAAGCAAG

upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaa-tgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
||  |||  |   |  |||    |||||||| ||   | |   ||||||||||    |        | ||||| |||| | | |||||||||||||||||||| |||||||| ||||| |||||||||||  |||| |||||||| || || ||||||||| | ||||||||||||||| | ||| | | 
gtcagtcccc---acttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG

upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 11
--------gtttgtcttccatatctatcaata-tgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
            | || |  || || |   || |  |   | |       | | ||||| |||   |||||    |        |      || |   ||||||| ||  |||||||||||||||| |||||||||||  |||| ||||||||  | ||||| || || ||||| |  || |||||  | ||| |  |
tccctcgaagaaggctactgtagctgtatctactacacatgacggtagccgtacatggatcaatatgtcttttaataactttattcattgtttgttttagGGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGA

upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------gtttgtcttccatatctatcaatatgtattagg-catggctt-------gaatatggaacaactagtcttagtgttct--aaatgtggaaacttttg-----acagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
                                                                        |    |||  | || |   || || | | | | ||| | ||       ||| |||    ||| | | | | |||| |  |   ||   |   ||||      |||||||| ||||||||||||||||| || || ||||||||  |||| ||||||||| |||| || || |||||||| |  || |||||    ||| |  |
gtatgggattcctatcgccttcctttctcttttatattcctctattatccagtaattccctatactttctcttcaaacttgtaaatttgagaaaatctttgatgtcatagtttttcatgcgaagatgttgaaaccaatgtaaatgtttttcagtggttacagtatttgctatggcagGGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGA

upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaa-atgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
                                             |   |||  | |     | |  ||| | || |     ||  |  ||||| ||  |||||||||||||||| |||||  | |||||||||||||||||||||||| || | || || |||||    |  || ||    |      |
------------------------------------------gtaagaaaactgcaaagtccattaatctcatatttcttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA

upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32324 (Selaginella moellendorffii), 3'ss of exon 8
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaa-atgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
                                             |   |||  | |     | |  ||| | || |     ||  |  ||||| ||  || ||||||||||||| |||||  | |||||||||||||||||||||||| || | || || ||| |    |  || ||    |      |
------------------------------------------gtaagaaaactgcgaagtccattaatctcatatttcttggctgcttccagGGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTTCCAGACGCATAATCGATAACGTAGA

upper sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ20930 (Selaginella moellendorffii), 3'ss of exon 7
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaa-caactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
                                   |      | |    |  | | |  |   | | || ||  | | |   ||  |  ||||| ||  || ||||||||||||| |||||  | |||||||| ||||||||||||||| || | || || |||||    |  || ||    |      |
----------------------------------gtaagaaaactgcaaagtccattgattccaatcttatatttcttgg--ctgcttccagGGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTTGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA

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|193724330|gb|FK657590.1|FK657590
EST:     TCATCGAACTATGCTCG                         GGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
genomic: TCATCGAACTATGCTCGgtttgtcttc ... cttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
EST: gi|9985118|gb|BE659226.1|BE659226
EST:     ATCCATGTGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCG                         GGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
genomic: ATCCATGTGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCGgtttgtcttc ... cttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
EST: gi|193529120|gb|FK484311.1|FK484311
EST:     ATCCATGCGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCG                         GGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
genomic: ATCCATGTGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCGgtttgtcttc ... cttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
EST: gi|13481114|gb|BG510457.1|BG510457
EST:     ATCCATGTGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCG                         GGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
genomic: ATCCATGTGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCGgtttgtcttc ... cttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
EST: gi|193571532|gb|FK532763.1|FK532763
EST:     GGAGTGTTGGATGTATTCTCATTGAACTATGCTCG                         GGGGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
genomic: GGAGTGTTGGATGTATTCTCATCGAACTATGCTCGgtttgtcttc ... cttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
EST: gi|22933892|gb|BU551031.1|BU551031
EST:     ATCCATGTGATTTGTGGAGTGNNNGATGTATTCTCATCGAACTATGCTCG                         GGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
genomic: ATCCATGTGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCGgtttgtcttc ... cttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
EST: gi|207729049|gb|GD706385.1|GD706385
EST:     TGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCG                         GGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
genomic: TGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCGgtttgtcttc ... cttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG
EST: gi|120529842|gb|EH257976.1|EH257976
EST:     ATCCATGTGATTTGTGGAGTTTTGGAAGTATTCTCATCGAACTATGCTCG                         GGTGAAGCATTGTTTCAGACTCATGGAAACTTGGAGCACCTGGCAATGATG
genomic: ATCCATGTGATTTGTGGAGTGTTGGATGTATTCTCATCGAACTATGCTCGgtttgtcttc ... cttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
                              ttctaaa  putative branch site (score: 2)
                                             ctttt  putative PPT
                              ttctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA