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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggcttttactatggtttgttagtcttggaaaagtatcctgtgctctttctattttctgtttggctaacttactttgacccatgttgtatttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAAGCTGTATTGCTATCTTCAACAGAGGCAGCTGAGATGATCCTTAGAGTTG

Basic information

species Glycine max
transcript GLYMA11G19220.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 11
caggctttta-ctatggtttgttag-tcttggaaaagtatcctgtgctctttctattttctgtttggctaacttactttgaccc-atgttgtatttc-tggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAAGCTGTATTGCTATCTTCAACAGAGGCAGCTGAGATGATCCTTAGAGTTG
 |    || | |||||   |   |  || ||     | |   ||   ||||  | ||  | ||||   |    || ||  ||   | ||| | | |  ||| |||| ||||| ||||| ||||  || || ||||||||||||||||| ||||| |||||||| || ||| | || ||||| ||||||||||| ||||||||||
-atatcttgatctatgtactagcatctcatgatctggaactttgctttcttgtttttaacagtttttttg---tatttaaacttgaggttttgtgtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAGGCTGTATTACTCTCTGCCACTGAGGCTGCTGAGATGATTCTTAGAGTTG
















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|16996964|gb|BM086336.1|BM086336
EST:     AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
EST: gi|15285688|gb|BI469579.1|BI469579
EST:     AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
EST: gi|31305141|gb|CD390344.1|CD390344
EST:     AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
EST: gi|254325805|gb|GR838686.1|GR838686
EST:     AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
EST: gi|254321099|gb|GR827548.1|GR827548
EST:     AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
EST: gi|31561195|gb|CD487033.1|CD487033
EST:     AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
EST: gi|6481479|gb|AW200750.1|AW200750
EST:     AGCATCAGAAGGAGGGCTGTTCTTCTGGAATTTATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
EST: gi|15815109|gb|BI787384.1|BI787384
EST:     AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
EST: gi|18735298|gb|BM528684.1|BM528684
EST:     AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCT                         GTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA
genomic: AGCATCAGAAGGAGGGCTGTACTTCTGGAATTGATGTTATTTCTGGCTCTgtaagtactg ... tttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctattttctgtttggctaacttactttgacccatgttgtatttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAAGCTGTATTGCTATCTTCAACAGAGGCAGCTGAGATGATCCTTAGAGTTG
                                           tatttct  CT-rich tract
      tattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caggcttttactatggtttgttagtcttggaaaagtatcctgtgctctttctattttctgtttggctaacttactttgacccatgttgtatttctggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAAGCTGTATTGCTATCTTCAACAGAGGCAGCTGAGATGATCCTTAGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - -tggtttg
- - - - - - - - - - - - - - -gaaaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgta