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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaagcttaaaatgataatgagttactctaacaccttgttatactttttggatcttatgaggtttcctcactccctttgggtgtgaggcaaattc...

Basic information

species Glycine max
transcript GLYMA08G43230.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G43230.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g72205.1 (Oryza sativa), 5'ss of exon 4
GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaagcttaaaatgataatgagttactctaacaccttgttatactttttggatcttatgaggtttcctcactccctttg---ggtgtga-ggcaaattc----
 | || || || ||||| |||   ||    | | | |||||  ||||| |||| |||||||| |||||||| || ||||||||||||||| |||  ||   ||||  | || ||    ||  || | |      ||  ||   || || |||   | || |  |    || |   | | | |  ||| | |     
ATTGCTAACCACCTTGATCGTGCTGTTAGTAGCTTGGGAAGGGATCCTTTGAAAGTTTTGGTACAAGTAAACACTAGTGGAGAAGAATgtgagtacag---aaaaaaaaaacgaaaatcttgaaaatccc----tatcttgaagacct-atggaatctcatttcctgtttagcttgatctaatagcatagttttag

upper sequence: GLYMA08G43230.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv19s0090g00910.t01 (Vitis vinifera), 5'ss of exon 4
GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaagcttaaaatgataatgagttactctaacaccttgttatactttttggatcttatgaggtttcctcactccctttgggtgtgaggcaaattc---------
 | |||||||| ||||| ||| |||| |||  | |  |||| || ||| ||||||||||||| ||||| ||||| |||||||||| |||| ||| ||    |||   ||        |||| |    ||   | |  ||  ||||   ||| | |     | |     | |   ||  |    | ||          
ATTGCAAATCAGCTTGATCGTGTGGTTTCAGGCATCAGAAGGAAGCCTTTGAAGGTTTTGGTTCAAGTGAATACTAGTGGAGAAGTATgtgagtaaaatcaaaaccaat--------actccattggctatgtttggttcctggaaagtatcaagaaaa-taaaaatttgttaatgaaaaatgattttctcatgctt
















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|208172293|gb|GD968910.1|GD968910
EST:     AGAAATCCTCTGAAGGTTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AGAAATCCTCTGAAGG-TTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|298199617|gb|HO043494.1|HO043494
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAACACATG
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATG
EST: gi|209708248|gb|BW678618.1|BW678618
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCC
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCC
EST: gi|120530250|gb|EH258384.1|EH258384
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|20498376|gb|BQ273306.1|BQ273306
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCTAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|209728275|gb|BW658487.1|BW658487
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|21285679|gb|BQ473550.1|BQ473550
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|298165006|gb|HO011055.1|HO011055
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCGACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|208064645|gb|GD865921.1|GD865921
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|13180762|gb|BG352102.1|BG352102
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|208156781|gb|GD957287.1|GD957287
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACA
EST: gi|298163042|gb|HO011775.1|HO011775
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|298179673|gb|HO024888.1|HO024888
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGT
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGT
EST: gi|193664931|gb|FK610891.1|FK610891
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|15664325|gb|BI701696.1|BI701696
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCTAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|193353738|gb|FK319422.1|FK319422
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAA-CNTGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|209705383|gb|BW668013.1|BW668013
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|207845177|gb|GD816202.1|GD816202
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAA
EST: gi|21993868|gb|BQ785396.1|BQ785396
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|15337855|gb|BI498511.1|BI498511
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         C-AAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTG
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTG
EST: gi|17401932|gb|BM178714.1|BM178714
EST:     AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCTAAACATGTGA
genomic: AAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
EST: gi|22525413|gb|BU084224.1|BU084224
EST:     TAAATACGAGTGGAGAAGAAT                         CCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA
genomic: TAAATACGAGTGGAGAAGAATgtaagttaag ... attgttgcagCCAAATCTGGTATTGATCCTTCCAACTGTGTTGAGCTTGCAAAACATGTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCAAATCATCTTGACCGTATGGTATCAACCCTTGGAAGAAATCCTCTGAAGGTTTTGGTGCAAGTAAATACGAGTGGAGAAGAATgtaagttaagcttaaaatgataatgagttactctaacaccttgttatactttttggatcttatgaggtttcctcactccctttgggtgtgaggcaaattc

- - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA