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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattcatggatgtactcgtgttttgaaccatttttctgcacatgatttactgcataatgaatgttgattaaacatattctttctctattttaaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCACTCCAAGCAACAGAAGAGGGGTTTATTTCGGTGGTTGCCAGACAGTTTTC

Basic information

species Glycine max
transcript GLYMA20G24100.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 2
-cattcatggatgtactcg--tgttttgaaccatttttctgcacatgatttactgcataatgaatgttgattaaacatattctttctctattttaaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCACTCCAAGCAACAGAAGAGGGGTTTATTTCGGTGGTTGCCAGACAGTTTTC
  |||  |  ||    | |  |||| |  |  | |    | |   |  |    |  | |   | |  | |||||   |  | |||   ||||||   || |||| || ||||||||||| ||||| |||||   ||||||||| ||||||||  | ||||||||||||||||||||||| ||  | ||||| |||||||  ||
ctattgctcaattactttgactgttgtagattactgaagttctagttctaggttagagatcaattccttattaactcttctgttttggtatttt---ttacagGGTTTACTTCAGAGCAGCAATCCATGTCAACGGATGTAATACGCAAGGCTTTTCAAGCAACAGAAGAGGGGTTTATCTCTCTTGTTGCTAGACAGTGGTC
















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|10238100|gb|BE806988.1|BE806988
EST:     GCCCGAGACATCGCGGTTTATCAATGATCACCTATTTCACCATCTCAAGA                         GATTTACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
genomic: GCCCGAGACATCACGGTTTATCAATGATCACCTATTTCACCATCTCAAGAgtaagttggc ... taaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
EST: gi|17519473|gb|BM188515.1|BM188515
EST:     GCCCGAGACATCACGGTTTATCAATGATCACCTATTTCACCATCTCAAGA                         GATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
genomic: GCCCGAGACATCACGGTTTATCAATGATCACCTATTTCACCATCTCAAGAgtaagttggc ... taaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
EST: gi|308098935|gb|HO760776.1|HO760776
EST:     GCCCGAGACATCACGGTTTATCAATGATCACCTATTTCACCATCTCAAGA                         GATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
genomic: GCCCGAGACATCACGGTTTATCAATGATCACCTATTTCACCATCTCAAGAgtaagttggc ... taaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
EST: gi|193436356|gb|FK400800.1|FK400800
EST:     TCACCTATTTCACCATCTCAAGA                         GATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
genomic: TCACCTATTTCACCATCTCAAGAgtaagttggc ... taaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
EST: gi|7924076|gb|AW830084.1|AW830084
EST:     CCGAGACATCACGGTTTATCAATGATCACCTATTTCACCATCTCAAGA                         GATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC
genomic: CCGAGACATCACGGTTTATCAATGATCACCTATTTCACCATCTCAAGAgtaagttggc ... taaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactgcataatgaatgttgattaaacatattctttctctattttaaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCACTCCAAGCAACAGAAGAGGGGTTTATTTCGGTGGTTGCCAGACAGTTTTC
                tgttgat  putative branch site (score: 4)
                             tattctttctctattt  putative PPT
                  ttgattaaacatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattcatggatgtactcgtgttttgaaccatttttctgcacatgatttactgcataatgaatgttgattaaacatattctttctctattttaaatttcagGATTCACTTCAGAGCAACAATCAATGTCGGTGGATGTAATTCGCAAGGCACTCCAAGCAACAGAAGAGGGGTTTATTTCGGTGGTTGCCAGACAGTTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
cattcat
- - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - tgcacat
- - - - - - - - - - - - - - - - - - - - - - - - - tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt