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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG

Basic information

species Glycine max
transcript GLYMA07G08320.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                              ||| |  | |  ||   |   || |||      ||  ||  | |||||  ||| ||   ||   | |    |||| ||||       ||||| | ||||| ||||| || ||||||||||| ||||||||||||||||||||   |||||| || || |||||||| |||||||| ||||||||||||
------------------------------gtttctatctcctgtcatcc-attagagacagtaa--tttaggtctgtggactgatccatttcttgtttttttttcttat-------tatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 9
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                                      ||||   | |   |||| |       ||      |  ||  |||||  |     ||| |     |||    | |  | | |  | | ||||| || || || ||||| ||||| ||||||||||||||||| ||   |||||| ||||| |||||||| ||||| || ||||||||||||
--------------------------------------gtttgcatctgctatcaaatgccatgaaaccac-tggtga-tactttgtagactaatgtttttctttcccttttgatccaa--gATTTTGGGTACTCCAACAAGAGAGGAAATCAGGTGCATGAATCCAAATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                    | || || ||| |  |   |  ||   |   ||||  ||       || ||  | |||   || | |  ||   |||   ||||  | ||  |       || | ||||| || || || ||||| || || ||||||||||||||||| ||    ||||| ||||| |||||||| ||||| || ||||||||||||
-------------------gtttgcat-ctgctatcaaatcgtgtcatgaaatca--ct------ggtggtactttgtaggctgaatgttttt-tcttctctttcttcatcca-------agATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctat-agGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                                     |  ||  | | ||     |  || |   |  | | ||||   || ||| ||    | | |      | ||  ||||| ||||  || |  | || || || || |||||||||||| |||| |||||||| || ||||  || || ||||||||||| || ||||||||||| |||||||||
------------------------------------gtacttaacctgatccctcgtgttccttcatctctcttcta--tatttaatttactagttta----ctcatc-tgtacatctaccagATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 9
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                       || | || |    | | ||| || | |  |||  |||||     || | ||     ||    |    | |    ||  || |   ||||  |    ||| |  |||| |||||||||||||||||||| | ||||||||||||||| |||||||| || |||||||| || || |||||||||||||||||||||
-----------------------gtttgctatcaagtggcttttctgt-tattca--ctttc-----ttttcttaatattataggtcagctaagcaggatgttgttgcatgttatgtcttagATTCTGGGTACACCCACCAGAGAAGAAATTAAGTGCATGAATCCAAATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------gtacattttttttgtgttcttctgtat--actgttcccttgttttgct---ttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagctttta----ttatg--tactt-----cta----tagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                                                      || |   | ||| |  ||  || || |  | ||||   |||  |||     || |     |   || |   ||    |  |   || | | |||   |   ||    | ||    |||||  || ||      ||    ||||| ||||| ||||||||  | || || |||| |||||||||||| |||||||  || || ||||||||||| ||||| ||||| || |||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagtta-tgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-----gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctat---agGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
     | |||     |    | | || |||  |  | |  | |  || ||||  || |      |      |  ||||| ||          | |  | | |  | | ||       | || | |   |||| ||||| ||||| ||  | || || || | |||||||||||| |||||||  || || |||||||| || || || ||||||||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtactt-gcttgctggttgtgactgttgcgggagtgttatgatg------ctgtggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------gtacattttttttgtgttcttctgtatactgttcccttgttttgct-ttatgatcagactttccaaagttgtgttctgtctac-ttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                                                                     |   |    | |||| || |  |  |   ||||  ||  | ||| |  |  |    |  || |     | | |        |   | |       ||  |       ||  || |  |  | |||| || || ||||| ||  | || || |||| |||||||||||| |||||||  || || ||||||||||| ||||| |||||||| |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtg-atgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagctt--ttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                                                 |   ||  | |||    | | | || | |||  || ||| | | |   |  |||  | |  |  | ||| |  ||||||| || || || ||  | || ||||| |  |||||||||||||||||||  || |||||||| |||||||||||||| || || |||||||||
------------------------------------------------gtacgcatgcattct--tgctcttttttttctgttt-tttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagctt--ttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                                                       |         | |  || ||| | |  || ||| | | |   |  |||  | |  |  | ||| |  ||||||| || || || ||  | || ||||| |  |||||||||||||||||||  || |||||||| |||||||||||||| || || |||||||||
-------------------------------------------------------gtacgcatgcattcttgctctcttt-tttctttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

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|193510758|gb|FK471246.1|FK471246
EST:     CATTGTTTCCTGGAGAGAGTGGGGTTGATCAGTTAGTTGAGATCATTAAG                         GTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
genomic: CATTGTTTCCTGGAGAGAGTGGGGTTGATCAGTTAGTTGAGATCATTAAGgtacattttt ... acttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
EST: gi|208189255|gb|GD985633.1|GD985633
EST:     CATTGTTTCCTGGAGAGAGTGGGGTTGATCAGTTAGTTGAGATCATTAAG                         GTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
genomic: CATTGTTTCCTGGAGAGAGTGGGGTTGATCAGTTAGTTGAGATCATTAAGgtacattttt ... acttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
EST: gi|8827250|gb|BE210980.1|BE210980
EST:     CATTGTTTCCTGGAGAGAGTGGGGTTGATCAGTTAGTTGAGATCATTAAG                         GTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC
genomic: CATTGTTTCCTGGAGAGAGTGGGGTTGATCAGTTAGTTGAGATCATTAAGgtacattttt ... acttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
                                            tacttct  CT-rich tract
                                  ttttattatgtactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA