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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatctttcttctttcctttgtttatttttcttattttattaatattcaagtctcatgaaaggcatcatagtaagttgcactttttgcttgcactgctatcttgacatggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATACCTACAAAAGACAATCGGAGGCTGCTGCATAATTTTATTACTGGTGTTA

Basic information

species Glycine max
transcript GLYMA05G25780.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 9
gtaaggatctttcttctttcctttgtttatttttcttattttattaatattcaagtctcatgaaaggcatcatagtaagttgcactttttgcttgcactgctatcttgacatggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATACCTACAAAAGACAATCGGAGGCTGCTGCATAATTTTATTACTGGTGTTA
                     |  |   ||||||| |   |  || | |||  |  |   |||||   |  | |  ||  |    ||||| |||||     | | ||| | |  | ||||| |||| |  || ||||||||| |||| ||||||||||||||||| || || |||||||| ||||||||  ||||||||||||||||| || ||||  || 
--------------------gtaagcagatttttccttgatgcttcaaatttta--caagtgaaaaatacta-atgaatctctcttttttacttgc----ttgtgttgtcctc-tctgcagATATCCCTCCGCCTTTTTGAACTAACCAATACACTTAAGACAGTTTTTATTCCTACAAAGGACAATCGCCGGCTGCTGCATAATTTTCTTGCTGGAATTG
















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|192332806|gb|FK026807.1|FK026807
EST:     TCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: TCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|254338250|gb|GR849775.1|GR849775
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|58014756|gb|CX701498.1|CX701498
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|193565843|gb|FK526348.1|FK526348
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|51337283|gb|CO981149.1|CO981149
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|192300083|gb|FG991873.1|FG991873
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|208326566|gb|GE124910.1|GE124910
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTCAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|207688258|gb|GD672597.1|GD672597
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATTTCATCG
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCG
EST: gi|31463811|gb|CD405839.1|CD405839
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|192332805|gb|FK026806.1|FK026806
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
EST: gi|26057405|gb|CA800319.1|CA800319
EST:     CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT                         GTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA
genomic: CGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTgtaaggatct ... tggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatcatagtaagttgcactttttgcttgcactgctatcttgacatggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATACCTACAAAAGACAATCGGAGGCTGCTGCATAATTTTATTACTGGTGTTA
                                     tcttgac  putative branch site (score: 3)
     atagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatctttcttctttcctttgtttatttttcttattttattaatattcaagtctcatgaaaggcatcatagtaagttgcactttttgcttgcactgctatcttgacatggtttgcagGTATCTCATCGACTTTTTGAATTAACAAATACACTTAAGACAGTGTTCATACCTACAAAAGACAATCGGAGGCTGCTGCATAATTTTATTACTGGTGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC