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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatttatgatatttcattcattaatcttcttttgatataaaaaaggattaattatttaattaccatctaatcatttatttgtaataattaattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTTCCTGTGTCATGTACCCAACATGTTGGAAATGAAAATGGAGCTGATTACT

Basic information

species Glycine max
transcript GLYMA07G02120.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G02120.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g04120.t01 (Vitis vinifera), 3'ss of exon 8
tcatttatgatatttcattcattaatcttcttttgatataaaaaaggattaattatttaattaccatctaatcatttatttgtaataattaattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTTCCTGTGTCATGTACCCAACATGTTGGAAATGAAAATGGAGCTGATTACT
     ||| |||| | |  ||||  || |   |  || ||   ||    |||  |   |||| |    |  | |    | |||  | ||  ||   | ||||  || |||||   |||| ||||||||||||||||||| ||||| ||||||| || || || || || || ||||||| ||| |||||||| ||||| |
----gtat-atatat-acgcattcctccttgctcaat-tattcaaaatctaaaaa---aatttcggcttttttaaccttctgttcttatatatattttagGATACACAAGATGCACCAAAGGACTTGAAGAGTAGAGGGTTGTGCCTGGTTCCGGTTTCGTGCACTCAGCAGGTTGGAAGTGACAATGGAGCCGATTATT
















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|22522662|gb|BU081473.1|BU081473
EST:     CTGTTGAATGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAG                         GACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
genomic: CTGTTGAATGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAGgtattctttc ... aattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
EST: gi|13312684|gb|BG406335.1|BG406335
EST:     CTGTTGAATGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAG                         GACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
genomic: CTGTTGAATGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAGgtattctttc ... aattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
EST: gi|58025145|gb|CX711886.1|CX711886
EST:     TGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAG                         GACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
genomic: TGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAGgtattctttc ... aattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
EST: gi|213608378|gb|DB974950.1|DB974950
EST:     GTCAGCTGTTGAATGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAG                         GACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
genomic: GTCAGCTGTTGAATGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAGgtattctttc ... aattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
EST: gi|207819971|gb|GD793349.1|GD793349
EST:     ACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAG                         GACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
genomic: ACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAGgtattctttc ... aattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
EST: gi|209722358|gb|BW665844.1|BW665844
EST:     CTGTTGAATGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAG                         GACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT
genomic: CTGTTGAATGACAATGGCCTGAAAAGAAAGGGAGCTCCAAACCAGgtattctttc ... aattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattaattatttaattaccatctaatcatttatttgtaataattaattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTTCCTGTGTCATGTACCCAACATGTTGGAAATGAAAATGGAGCTGATTACT
                                         aattaat  putative branch site (score: 3)
     aattatttaattacca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatttatgatatttcattcattaatcttcttttgatataaaaaaggattaattatttaattaccatctaatcatttatttgtaataattaattaatcagGACGCAAAAGATAAGCCAAGGGACTTGAAGAGTAGAGGGCTGTGCTTGGTTCCTGTGTCATGTACCCAACATGTTGGAAATGAAAATGGAGCTGATTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - -cattcat
- - - - - - - - - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatcta