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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accatctcagaattggttcttatttgaatgtaattttttttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG

Basic information

species Glycine max
transcript GLYMA13G20930.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 7
accatctcagaatt-ggttcttatttgaatg--taattttttttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG
|     |  || ||  |    |||||| |    || |  |||  | |    ||   ||  |||  || |      ||| |  | |   |    | |  | |||| ||||||||||||  |||  |||| ||||| |||||| ||||||||||||| || || |||||||||||||| || || |||
aaggcttgtgacttcagagaatatttgcaccattattaatttgatgccagctaggatgtggcaatatgcct---cactgattttatgattcgttctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG

upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 7
accatctcagaattggttcttatttgaatgtaattttt--tttttcagaatacagtgcagcagcattctagaatactaaca--tcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG
   || |     ||   | |||||| | |||  || |    | || |   |||       | ||  | |     ||| ||    |    |    ||| || |||| ||||| ||||||  |||| |||| ||||| |||||| |||||||||||||||| ||||||||||||||||| || || |||
---atgttctg-ttaaattttatttcagtgttgttgtggggtgtttaacgtacttactgactgcgatgtgaccaactgaccatcctcctttgcttgtgttgcagGTTCTGTGAATGCAGCCAACTGTGCGGAGCTAGCAAAGAAAGAAGATATTGATGGTTTTCTTGTTGGTGGTGCCTCTTTGAAG

upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G852968_T03 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------------------------accatctcagaat--tggttcttatttgaatgtaatttttt--------ttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG
                                                                                    | ||  |||   |||||   | ||   |  | |  | |          |    || |  |       ||  | |    |    |  |  |  |  ||||| || |||| ||||| ||||||  |||| |||| ||||| |||||| |||| ||||| ||||| ||||||||||||||||| || || |||
gttggtttctcgtttcacataagctgtcaggataacgtgtttcgcgtgtttctttttccattaaatttgaaaatggaaagattgaacttggaaccgtggtttgcagtttgctaaattactatgaggataacgtgtttaacatggcttgatggccctgtgatgtgaccatcttcatttgctctgtgttgcagGTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG

upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
accatctcagaattggttcttatttgaatgtaattttttttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG
                    |   | |   || || | | |  || |||     | | |   ||  | || || |  | ||  | |        |  |||| ||||| |||| | |||||||||| |||||||| ||  ||||||| |||||||||||||||||||||||||| || || |||
-------------------gtgcgttagattagttatctgtcgcaaaat-----gaaactttatgtt-gattattgccttctcaat--------tgccagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG

upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 7
-accatctcagaattggttct--------tatttgaatgtaattttttttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG
    || ||| |  | ||| |        | | |||||||   |  |||| |    || | || |||  |||| ||  |    |   ||||||    ||| | || |||| || || ||||  |||||  || | ||||| || || ||||| ||||||||||||||||||||||| |||||||| ||||||
ttggatgtcaaatgtagttttatactctgtgtctgaatgtt-ctggttttctggagatgctgtccagt-gcatgctgca----tctgatcaaac---tctcttttgcagGTTCAGTGAATGGGAGCAATTGTTCAGAGCTCGCCAAACAAGAGGATATTGATGGATTTCTTGTTGGCGGTGCTTCCTTAAAG

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|208286741|gb|GE085315.1|GE085315
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCGAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|208199925|gb|GD998612.1|GD998612
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|193565354|gb|FK522821.1|FK522821
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|208158835|gb|GD958252.1|GD958252
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|193716815|gb|FK654653.1|FK654653
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|207752026|gb|GD722143.1|GD722143
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAA                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|208133444|gb|GD929123.1|GD929123
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|208220559|gb|GE017135.1|GE017135
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|193532323|gb|FK491989.1|FK491989
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|193404769|gb|FK368282.1|FK368282
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|207841384|gb|GD811420.1|GD811420
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|151399754|gb|EV269625.1|EV269625
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|207816408|gb|GD786241.1|GD786241
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|208215434|gb|GE012463.1|GE012463
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|193632944|gb|FK580092.1|FK580092
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|193679131|gb|FK620625.1|FK620625
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGTAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|193703433|gb|FK636505.1|FK636505
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|208240804|gb|GE036834.1|GE036834
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
EST: gi|193730132|gb|FK663090.1|FK663090
EST:     GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACATGAATTATTTATGGAG                         GATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG
genomic: GAAGAATGTCTCAGCTAAAGTTGCATCTAAAACACGAATTATTTATGGAGgtacattaac ... tgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG
                          tactaac  putative branch site (score: 0)
                                           tctgtctttc  putative PPT
                        aatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accatctcagaattggttcttatttgaatgtaattttttttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
-ccatctc
- - - - - - - - - - - - -gaatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaca