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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgcttgatgggcgacagagtaagtacttgctgttaacgattgatggtaacaatgtagttactgaagctccttttttatgttttctttcccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAATCATGGAGTGTGAAAGCTGGACCAGGG

Basic information

species Glycine max
transcript GLYMA19G32990.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G32990.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------tgtgcttgatgggcgacagagtaagtacttgctgttaacgattgatg-gtaacaatgtagttactgaagctccttttttatgttttctttcccttg--tgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAATCATGGAGTGTGAAAGCTGGACCAGGG
                                                       |  |  || |    ||   |  | |   | |||    | ||| |  || | ||| ||  | |     |  |  |||| | || |  ||   |||  || ||||||||||| | |||| |||||||||||| || || |||||||| || ||||||||||| ||||||       |||||||                    
gtacaccactttcttgtcttccattcatacaaaaagcacataaccattcgaatcattttcaatagtaatcaccttggg-atccgatgt--gtggttgctaagttaaaatataagt-ccatgacaacaattttgtcttgtggttgttttgattgcagATGTGGATTTCAAAGGGAGAGTATGATGAGTCAGGGCCATCAATTGTTCACAGGAAATGTTTCTAA-------TCATGGA--------------------

upper sequence: GLYMA19G32990.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 5
--------------------------tgtgcttgatgggcgacagagtaagtacttgctgttaacgatt--gatggtaacaat-gtagttactgaagctccttt----ttta---tgttttctttcccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAATCATGGAGTGTGAAAGCTGGACCAGGG-
                          ||   ||  ||          |   | | ||   ||     ||   ||| |  |  | || |   ||| |     | |    ||||    |||| |||    | ||| ||||||||||||||||| | ||||| ||||| || || |||||||| || |||||||| || |||||    |     |   | | |      |    |||   
gtaatgtatttgactcgtgtctgagttgcatttcgtgtttttttttatgtcttcatgtctttgtttcttcaaatgctcgcgtttgtcgaggctgtaatctttctggaatttaatccgtttacttgttgtggtgcagATGTGGATTGCGAAGTCGGAGTACGATGAGTCAGGTCCATCAATTGTGCACAGGAAGTGTTTCTAGAGCAGTGCGACACA-TCTTTTGCTTTTTTCAGCAC
















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|208059642|gb|GD860346.1|GD860346
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|192303906|gb|FG998258.1|FG998258
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|207738285|gb|GD713739.1|GD713739
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|17153513|gb|BM143446.1|BM143446
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|6725381|gb|AW309780.1|AW309780
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|192328623|gb|FK020813.1|FK020813
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCTCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAAGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|6719298|gb|AW306945.1|AW306945
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|207763988|gb|GD738419.1|GD738419
EST:     GTGTCTGGATCGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|7795522|gb|AW780919.1|AW780919
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCTTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|9985773|gb|BE659881.1|BE659881
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|31309553|gb|CD394756.1|CD394756
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|13252153|gb|BG363056.1|BG363056
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|9259066|gb|BE347213.1|BE347213
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|192330415|gb|FK021188.1|FK021188
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGC
EST: gi|208216330|gb|GE009406.1|GE009406
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|12774751|gb|BG239678.1|BG239678
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|6912916|gb|AW394446.1|AW394446
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|7639397|gb|AW733721.1|AW733721
EST:     GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCCATCTTGGCTTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtaacaatgtagttactgaagctccttttttatgttttctttcccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAATCATGGAGTGTGAAAGCTGGACCAGGG
                       ctccttttttatgttt  CT-rich tract
                           ttttttatgttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgcttgatgggcgacagagtaagtacttgctgttaacgattgatggtaacaatgtagttactgaagctccttttttatgttttctttcccttgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAATCATGGAGTGTGAAAGCTGGACCAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- tgcttga
- - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - -gatggta
- - - - - - - - - - - - - - - - - - - - - - - - - -caatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttactg