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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatattgatatttttccatcaattgatcattatggcatgattgtagattttgattggtgaatgatctttgcttatggttggctttttttttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG

Basic information

species Glycine max
transcript GLYMA17G05530.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05530.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 9
ttatattgatatttttccatcaattgatcattatggcatgattgtagattttgattggtga----atgatctttg--cttatggttg-gctttttttttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG
     ||| |  || | |||   |||||    ||| |    ||      |||  ||    |     | ||| | |  ||||   |     |  | ||| || || |||||||||  |||| |   | ||||||||  |||| ||||| |||| ||| ||||||||||||||||||||||||||||||||||||
----cttgctggttctgcat---ttgatatggatgtccgagtttggagctttactttacaacattgttatcatagaccttacaatcatagtactctttcttgtgcagAAGATGGGAAAGACAAGTCAAATGATGAAGCTCCAGAGAACAATCTTCAGTATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG
















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|15285660|gb|BI469551.1|BI469551
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|208267978|gb|GE072949.1|GE072949
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|208039111|gb|GD835865.1|GD835865
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|193616957|gb|FK571627.1|FK571627
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTACAA
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCT-CAA
EST: gi|193490170|gb|FK455505.1|FK455505
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|13312169|gb|BG405829.1|BG405829
EST:     TTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAA-AAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: TTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|26058248|gb|CA801162.1|CA801162
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|208052705|gb|GD850028.1|GD850028
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|208146424|gb|GD946261.1|GD946261
EST:     TTGACCAATGGATCATCT-                         --GATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: TTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|6072359|gb|AW101746.1|AW101746
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|207708411|gb|GD691409.1|GD691409
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|24136117|gb|BU926627.1|BU926627
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|193500769|gb|FK464566.1|FK464566
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|207745466|gb|GD714028.1|GD714028
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|193632381|gb|FK584191.1|FK584191
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAA
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAA
EST: gi|208150143|gb|GD950790.1|GD950790
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGACCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|208325993|gb|GE119703.1|GE119703
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAGGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|21637806|gb|BM107961.1|BM107961
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
EST: gi|193624299|gb|FK573395.1|FK573395
EST:     GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTG                         AAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT
genomic: GCAGACTTCAGATTCGAGAAGTGTCGTGGAGTTGACCAATGGATCATCTGgtgagattga ... ttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattttgattggtgaatgatctttgcttatggttggctttttttttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG
   ttttgat  putative branch site (score: 4)
                                 ttggcttttttttttt  putative PPT
                                      tttttttttttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatattgatatttttccatcaattgatcattatggcatgattgtagattttgattggtgaatgatctttgcttatggttggctttttttttttttgtagAAGATGGCCAAGAAACAACCAATGATGACACTCCTGAGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG

- - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - -attggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgg