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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaatgctgcatgattctgtgaatgattgtcttcaatttggatgtttcagtgctgctaacctgggcttatggtcatgtctttttgtcaacaatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAAAGTTGAGTTTGGCCTTCCTGACTTAGAGAGTAGGACGCAGATATTCAAG

Basic information

species Glycine max
transcript GLYMA07G05220.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 8
gaaaatgctgcatgattctgtgaatgattgtcttcaatttggatgtttcagtgctgctaacctgggctta-tggtcatgtctttttg--tcaacaatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAAAGTTGAGTTTGGCCTTCCTGACTTAGAGAGTAGGACGCAGATATTCAAG
    ||  | |  |||     |  ||||| ||     ||||| | | |       ||| |  ||    || |    || |   ||||  | | || |||  ||||||||||| || |||||||||||  | || ||||| || || ||||| || |||||||||||||||||||| || |||||||| || |||||||| |||
---cataattctagatataaggtttgattttcaagtttttgggtctcttccactagcttagatgtctctacttacaatttaaatttggtttatcattttacagGCCTGACACACTTGATCCAGCACTGTTACGCCCTGGACGGTTAGACCGCAAGGTTGAGTTTGGCCTTCCTGATTTGGAGAGTAGAACACAGATATTTAAG
















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|209728032|gb|BW666754.1|BW666754
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|8284561|gb|BE022129.1|BE022129
EST:     GATGGGTTTGATGCTC-GGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|19937368|gb|BQ081261.1|BQ081261
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|16277271|gb|BI942294.1|BI942294
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCGACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGAGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|57575942|gb|CX548913.1|CX548913
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|192302202|gb|FG997282.1|FG997282
EST:     GATGGGTTTGATGCTCGGGGAACCATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|207771905|gb|GD745676.1|GD745676
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTATTAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|58024535|gb|CX711276.1|CX711276
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|209728031|gb|BW666753.1|BW666753
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|209717333|gb|BW659036.1|BW659036
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|58021578|gb|CX708319.1|CX708319
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|163926888|gb|EH040053.1|EH040053
EST:     AGTTTTGATGGC-ACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: AGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|19269325|gb|BM885581.1|BM885581
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
EST: gi|7327091|gb|AW620889.1|AW620889
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagtgctgctaacctgggcttatggtcatgtctttttgtcaacaatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAAAGTTGAGTTTGGCCTTCCTGACTTAGAGAGTAGGACGCAGATATTCAAG
         tgctaac  putative branch site (score: 1)
                                                tttct  putative PPT
                                           aacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaatgctgcatgattctgtgaatgattgtcttcaatttggatgtttcagtgctgctaacctgggcttatggtcatgtctttttgtcaacaatttctagGCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAAAGTTGAGTTTGGCCTTCCTGACTTAGAGAGTAGGACGCAGATATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - -gcatgat
- - - - - - - - - - tgaatga
- - - - - - - - - - - - - - -gtcttca
- - - - - - - - - - - - - - - - - - - -tggatgt
- - - - - - - - - - - - - - - - - - - - - - - - - gtgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg