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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttacttcttttatttaagtaagttctggcattcttgaattaaatatgtaagaaaagtgaagagaagcttagtattagttgttgttcacaaaatat...

Basic information

species Glycine max
transcript GLYMA16G32990.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G173858_T02 (Zea mays), 5'ss of exon 3
TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatctt----acttcttttatttaagtaagttctggcattcttgaattaaatatgtaagaaaagtgaagagaagcttagtattagt-tgttgttcacaaaatat
|   ||| || || || |||||||||||  ||||||| || ||||||||||||   || || ||||||||||| |||||||| ||||||||||||| |      | | ||||   |      |   ||||    |   |||   | ||   | ||  || || ||  | |    | | | | ||| | | ||     
TTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaaagcctttttttactggtaggggattggctcgatatcattggttctgcttgtaac-tgcagtgacacatctggtcattctcttggtgataat----

upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G173858_T01 (Zea mays), 5'ss of exon 2
--------TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatctt----acttcttttatttaagtaagttctggcattcttgaattaaatatgtaagaaaagtgaagagaagcttagtattagt-tgttgttcacaaaatat
        |   ||| || || || |||||||||||  ||||||| || ||||||||||||   || || ||||||||||| |||||||| ||||||||||||| |      | | ||||   |      |   ||||    |   |||   | ||   | ||  || || ||  | |    | | | | ||| | | ||     
AGAAATAGTTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaaagcctttttttactggtaggggattggctcgatatcattggttctgcttgtaac-tgcagtgacacatctggtcattctcttggtgataat----

upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 2
TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatctt----acttcttttatttaagtaagttctggcattcttgaattaaatatgtaagaaaa-gtgaagagaagcttagtattagttgttgttcacaaaatat
|   ||| || || || |||||||||||  ||||||| || ||||||||||||   || || ||||||||||| |||||||| ||||||||||||| |      | | ||||   |      |   ||||    |   |||   | ||   | ||  |    || |    | ||  |   | ||| | | ||     
TTGTTCGGGCCATAGTGCCGAGAATGAATCTGGACGATCTCTTTGAGCAGAAGAACGATGTGGCCAAAGCTGTATTGGAGGAGCTTGAAAAGgtatttctaaagcctttttttactggtaggggattggctcgatatcattggttctgcttgtaactgcagtgacacatctggtcatttctcttggtgataa-----

upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0022g01690.t01 (Vitis vinifera), 5'ss of exon 3
TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttacttcttttatt--taagtaagtt-ctggcattcttgaattaaatatgtaagaaaagtgaagagaagcttagtattagttgttgttcacaaaatat
||  ||| |||  |||||| |||||||  ||||| ||||||||||| || |||||||| |||||  || | ||||||||||| ||||| ||||||  ||  | || |||    | | | | |   |   | |  |     || | |    ||||  || | |  |  ||    |   || | |||||   ||   
TGGTTCGAGCTCATGTTCCAAGAATGACTTTGGATGAGCTGTTTGAACAAAAGGGTGATGTTGCTCAAACCGTCTTGGAGGAGCTTGAGAAGgtaatttgatgctgttacagatgattgaatggttaatagtgatatgccaagttttatggaaagatgcatattaaattgacctatattttggttcattcaa---

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|298190343|gb|HO032464.1|HO032464
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|254327495|gb|GR837050.1|GR837050
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|213603197|gb|DB960460.1|DB960460
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|254346709|gb|GR856431.1|GR856431
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|192328203|gb|FK022882.1|FK022882
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|254323382|gb|GR835883.1|GR835883
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|298179574|gb|HO028045.1|HO028045
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|51345167|gb|CO985900.1|CO985900
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|209701321|gb|BW655916.1|BW655916
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|298184948|gb|HO030161.1|HO030161
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GCGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|298164789|gb|HO010786.1|HO010786
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|16347781|gb|BI973376.1|BI973376
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAA                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCCTGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|298197264|gb|HO042007.1|HO042007
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
EST: gi|120530546|gb|EH258679.1|EH258679
EST:     TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAG                         GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT
genomic: TTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttact ... catgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACTCGTGCTATTGTTCCGAGAATGAACTTGGACGAGCTGTTTGAGCAGAAGGGTGAGGTTGCCAAAGCTGTCTTGGAGGAACTTGAAAAGgtatcttacttcttttatttaagtaagttctggcattcttgaattaaatatgtaagaaaagtgaagagaagcttagtattagttgttgttcacaaaatat

- - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA