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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgcagatagtaattttactggacttgttaattctgacagaaaactctgatgggttgttttgtttggatcatatttaatgatttatgactaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG

Basic information

species Glycine max
transcript GLYMA08G07960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 2
----ttgt-gcagatagtaatt-ttactggacttgttaattctgacagaaaactctgatg---ggttgttttgtttggatcatatttaat--gatttatgactaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG
    |||| ||   | | |||| || ||    ||  ||| | |    ||    |||  |      | || ||   | | || ||| || |    ||| ||  |||   |||||||| |||||||| |||||||||||||| ||||||||||| || ||| || |  |||| |||||  | ||| ||||||| || ||    ||
gtcattgttgctcttcgaaattgtttctcagatttataagtgtttttgattgatctagtatccaatcgtcttagctag-tcttatgtagtttagtttctgtataa---cagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG

upper sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 2
----ttgtgcagatagtaattttactggacttgttaattctgacagaaaactctgatgggttgttttgtttggatcatatttaatgatttatgactaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG
       |||   ||  |   |  |   |     ||  |||  |  ||  || |       | ||| ||||  | | | | |      |||||  |   | |||||||| |||||||| |||||||||||||| ||||| || ||||||||| ||||  ||||||||||  | ||||  ||||| ||||| || ||
caataaatgcttttaacaccataccacaaaggagtagctctccctaaatcctttatattcatttttagtttttaccttgtgtg----cttatgggttcatccagGAACTATTTGAAGGATATTACTTCTGTCAAGCACAGAGGGAGGATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAG
















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|151410591|gb|EV280406.1|EV280406
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|298199306|gb|HO042669.1|HO042669
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|24135848|gb|BU926358.1|BU926358
EST:     ACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: ACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|298184831|gb|HO030044.1|HO030044
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCGG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|192328547|gb|FK023551.1|FK023551
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|298167316|gb|HO010755.1|HO010755
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|254330221|gb|GR839774.1|GR839774
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|298164922|gb|HO010919.1|HO010919
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|298167948|gb|HO013211.1|HO013211
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|22541663|gb|BU091506.1|BU091506
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|193422725|gb|FK385942.1|FK385942
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|298178170|gb|HO023905.1|HO023905
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
EST: gi|298187812|gb|HO031769.1|HO031769
EST:     GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAG                         GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT
genomic: GCTAGTTAGAGCTGCACATAAACAGGGTGCGAACATCATTCTCATTCAGgtctgcatat ... ctaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctgatgggttgttttgtttggatcatatttaatgatttatgactaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG
                                           gactaat  putative branch site (score: 2)
                        atcatatttaatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgcagatagtaattttactggacttgttaattctgacagaaaactctgatgggttgttttgtttggatcatatttaatgatttatgactaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
-tgtgcag
- - - - - - - - -ttactgg
- - - - - - - - - - - - - - - - -ttctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - tgggttg