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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttttcctttttaattttaaaaaattgtgattgaacatgatacctatcttatcctggtattataatagcatttacttttcttgccattatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG

Basic information

species Glycine max
transcript GLYMA10G04480.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G064695_T02 (Zea mays), 3'ss of exon 10
-------tattttttcctttttaattttaaaaaattgtgattgaacatgatacctatcttatcctggtatt--ataatagcatttacttttcttgccattatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG
        ||      | | ||  |||| |  |  |||| |   |  |    |  |  || | || ||| |  ||| ||   || | ||  |   || || |     ||||||  |||||||| || ||||| |||||  |||||||||||||||| || |||||||| || ||  | |||
aacaccccataaggatcatgtt--tttttaggacctgtgct---atgtatatctcaggtttttcttgtactgaatattattgttaatttgcccaaccgttgtc----agGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 10
---tattttttcctttttaat-tttaaaaaattgtgattgaacatgatacctatcttatcctggtattataatagcatttacttttcttgccattatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG
   ||  ||    || ||  |        |  |  | ||||    ||||  |   || | |||  | |||  |   | ||   ||  |||     || || |||||| |||| |||||||| || || ||||| || ||||||||||||||||| ||||||||||||||  |||||
atttaggttcagtttcttggtaccctctgacctaagtttgacttagataatttaatt-ttctgcaaatatgttctaactt---ttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG
















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|192311647|gb|FK004866.1|FK004866
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|192308760|gb|FG999785.1|FG999785
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|254325002|gb|GR834427.1|GR834427
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|17964783|gb|BM271512.1|BM271512
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|298179372|gb|HO027843.1|HO027843
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|18721747|gb|BM523360.1|BM523360
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|7326644|gb|AW620442.1|AW620442
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|51336677|gb|CO980543.1|CO980543
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|151406201|gb|EV276016.1|EV276016
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|6727069|gb|AW311423.1|AW311423
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAATGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT
EST: gi|12689320|gb|BG155656.1|BG155656
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGGTTG-AGTTCGTCTGGGAAGGCACCAATGTTG
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCA-GTTGTAGTTCGTCT-GGAAGGCACCAATGTTG
EST: gi|22523849|gb|BU082660.1|BU082660
EST:     TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAG                         GTTGCACTGAAAGTACCAGTTGTAGGTCGTCTGGAAGGCACCAATGTTGAT
genomic: TAATGAAGTGTGATGTTATAGCAAGTGGAATAGTGAATGCTGCAAAAGAGgttagtcaag ... tatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatcttatcctggtattataatagcatttacttttcttgccattatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG
                                cttttcttgccatt  CT-rich tract
               tattataatagcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttttcctttttaattttaaaaaattgtgattgaacatgatacctatcttatcctggtattataatagcatttacttttcttgccattatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - -gtgattg
- - - - - - - - - - - - - - - - - - - - tgatacc