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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacatataagttgtcattttcaattttcaccgtatgtttgaaaggaaacaacttaaaataattgaaattttgttttgttgcaattggtttgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAGATAGAAGAGGAGGTTGCAGCAGCAGCTGCAGTGGGATCTGGTGGGTTTG

Basic information

species Glycine max
transcript GLYMA20G30720.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30720.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0072g00380.t01 (Vitis vinifera), 3'ss of exon 1
acacatataagttgt-cattttcaattttcaccgtatgtttgaaaggaaacaacttaaaataattgaa--attttgttttgttgcaattg-gtttgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAGATAGAAGAGGAGGTTGCAGCAGCAGCTGCAGTGGGATCTGGTGGGTTTG
    | ||     ||   |  | || ||| |   ||| ||||     ||  || || | | ||  |||  ||||  | | ||    ||   | ||||  |||||||||||||||||||| | ||||||||||| |||||||| |||| ||||||||||||||| ||| |||| || || |||||||||||| |||| ||||| |
--gta-atgccccgtgtgtcatgaagtttgaaaatatttttgtttt-aattaattttatacaaaggaactatttcttatcgtcttgatgatgcttgaattatagCATGAGAAGCACAAGTCGGAGAAAGACCCTGAGCATGCCCACAAGCACAAGATAGAAGAAGAGATTGCCGCGGCTGCTGCAGTGGGAGCTGGCGGGTTCG
















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|5760292|gb|AI965655.1|AI965655
EST:     TTGAGCACCTTGGTGAGATAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAA
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAA
EST: gi|6915166|gb|AW396627.1|AW396627
EST:     TTGAGCACCTTGGTGAGTTAGGGGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAAGCAGAGAAAAGACCC-GAGCATGCTCACAAGCACAA
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAA-GACCCAGAGCATGCTCACAGGCACAA
EST: gi|192311586|gb|FK004841.1|FK004841
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAAGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|298166026|gb|HO008997.1|HO008997
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGA
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGA
EST: gi|19270861|gb|BM887117.1|BM887117
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|26057639|gb|CA800553.1|CA800553
EST:     TTGAGCACCTTGGTGAGTTAGGAGGTGCATCTGCTGCTGGTTACGCCTTG                         GATGAGAAGCACAAGGGAGAGAAAGACCC
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCC
EST: gi|26047174|gb|CA784047.1|CA784047
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|15814654|gb|BI786929.1|BI786929
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|207729133|gb|GD704901.1|GD704901
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|151407080|gb|EV276895.1|EV276895
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|19346614|gb|BM891494.1|BM891494
EST:     TGAGCACCTTGGTGAGGTAAGTGCTGCATCTGCTGCTGCTTACCGC-TTG                         CATGAGAAGCAC
genomic: TGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTAC-GCCTTGgtaatcttct ... tgatatatagCATGAGAAGCAC
EST: gi|16105859|gb|BI893599.1|BI893599
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|20448727|gb|BQ252851.1|BQ252851
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAAAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|5760534|gb|AI965897.1|AI965897
EST:     TGGTGAGTTAGGCGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|15199951|gb|BI424093.1|BI424093
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|8669768|gb|BE190875.1|BE190875
EST:     TTGAGCACCTTGGTGAGTAAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAT
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
EST: gi|192315155|gb|FK009979.1|FK009979
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCA
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCA
EST: gi|16106353|gb|BI894093.1|BI894093
EST:     TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTG                         CATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG
genomic: TTGAGCACCTTGGTGAGTTAGGTGCTGCATCTGCTGCTGCTTACGCCTTGgtaatcttct ... tgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacaacttaaaataattgaaattttgttttgttgcaattggtttgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAGATAGAAGAGGAGGTTGCAGCAGCAGCTGCAGTGGGATCTGGTGGGTTTG
                                          gtttgat  putative branch site (score: 5)
     aacttaaaataattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacatataagttgtcattttcaattttcaccgtatgtttgaaaggaaacaacttaaaataattgaaattttgttttgttgcaattggtttgatatatagCATGAGAAGCACAAGGCAGAGAAAGACCCAGAGCATGCTCACAGGCACAAGATAGAAGAGGAGGTTGCAGCAGCAGCTGCAGTGGGATCTGGTGGGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
acacata
- - - - - - - - - - - - - - - - - atgtttg
- - - - - - - - - - - - - - - - - - - - - - ggaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa