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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgcataacctattcttccattggtggatattttttaatttcctataaactttcagtatgattttagtattatattaactttgatgttttaaaattagGGGACAGCTTTTTCCATGACAGAACGAGATCGTCTTGATCTACGAGGACTGCTTCCTCCAAATGTTATGTCTCCTGACCTACAGATTGAACGATTCA

Basic information

species Glycine max
transcript GLYMA03G24630.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G24630.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0021g00500.t01 (Vitis vinifera), 3'ss of exon 1
ttttgcataacctattcttccat-tggtggatattttttaatt-tcctataaactttcagtatgattttagtattatattaactttg-atgttttaaaat-tagGGGACAGCTTTTTCCATGACAGAACGAGATCGTCTTGATCTACGAGGACTGCTTCCTCCAAATGTTATGTCTCCTGACCTACAGATTGAACGATTCA
   || |||||  || | |   | |  |    ||||  ||||  | || ||   ||  |   |      ||| |  | | | |||   || |  | | || ||||| || || || |||||||| |||||||||||||||||||| || ||||| || || ||||  |||||||| |||||  | || |||||||| ||||
---tg-ataactaatacattggtgttttttgaatttcctaataatgctttacttttataagttagggagagtttcttttcatcttcatatataatgacatgtagGGAACGGCATTCTCCATGACCGAACGAGATCGTCTTGATCTTCGTGGACTTCTCCCGCCAACAGTTATGTCCCCTGAAATGCAAATTGAACGCTTCA
















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|193387910|gb|FK354741.1|FK354741
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGACAGCTTTTTCCATGACAGAACGAGATCG
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGGACAGCTTTTTCCATGACAGAACGAGATCG
EST: gi|193382651|gb|FK345848.1|FK345848
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGACAGCTTTTTCCATGACAGAACGAGATCG
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGGACAGCTTTTTCCATGACAGAACGAGATCG
EST: gi|193379793|gb|FK345351.1|FK345351
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGACAGCTTTTTTCCATGACAGAACGAGATCG
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGGACAGCTTTTT-CCATGACAGAACGAGATCG
EST: gi|193385586|gb|FK349338.1|FK349338
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGACAGCTTTTT
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGGACAGCTTTTT
EST: gi|193305739|gb|FK269164.1|FK269164
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGACAGCTTTTTTCCATGACAGAACGAGATCG
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGGACAGCTTTTT-CCATGACAGAACGAGATCG
EST: gi|193305633|gb|FK270990.1|FK270990
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGACAGCTTTTTCCATGACAGAACGAGATCG
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGGACAGCTTTTTCCATGACAGAACGAGATCG
EST: gi|193311111|gb|FK275063.1|FK275063
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGGACAGCTTTTT
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGG-ACAGCTTTTT
EST: gi|193381654|gb|FK347077.1|FK347077
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGACAGCTTTTTTCCATGACAGAACGAGATCG
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGGACAGCTTTTT-CCATGACAGAACGAGATCG
EST: gi|193380604|gb|FK349234.1|FK349234
EST:     TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAA                         GGGACAGCTTTTTCCATGACAGAACGAGATCG
genomic: TCGTCCACAAACGCAGCCTTGACATTCTCCACGATCCTTGGTTCAATAAAgtatttcctt ... ttaaaattagGGGACAGCTTTTTCCATGACAGAACGAGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaactttcagtatgattttagtattatattaactttgatgttttaaaattagGGGACAGCTTTTTCCATGACAGAACGAGATCGTCTTGATCTACGAGGACTGCTTCCTCCAAATGTTATGTCTCCTGACCTACAGATTGAACGATTCA
             tatgattttagtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgcataacctattcttccattggtggatattttttaatttcctataaactttcagtatgattttagtattatattaactttgatgttttaaaattagGGGACAGCTTTTTCCATGACAGAACGAGATCGTCTTGATCTACGAGGACTGCTTCCTCCAAATGTTATGTCTCCTGACCTACAGATTGAACGATTCA

- -tgcataa
- - - - - - - ttcttcc
- - - - - - - - - - - -tggtgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt