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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtgttttgccttaatcaataaatgttttttattgcttttatatatttttacccttatctattaatatggtgtttgttaatttaactcccataa...

Basic information

species Glycine max
transcript GLYMA20G38860.1
intron # 49
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 49
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 13
GGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtgttttgcct-taatcaataaatgttttttattgcttttatatatttttacccttatctattaatatggtgtttgttaatttaactcccataa-
 || || ||||||||||| ||||| ||||||||  | ||||||||||| ||||| ||||||||||||||||| |||||||| |||||||| ||||||||||||| |    |||||||| ||    || |   ||||| ||||  | || |||||||   || ||      || |    |||  ||    ||  ||  ||   
CGTTGAGGATTTCAGAGACTGGACGAATTGGCTGTTTTACCGAGGTGGTATTGGGGTTAAGGGAGAAGAAAGTTGGGAAGCCTGGTGGGATGAAGAACTGgtaactga-attttgcctgtatatgattagcatttttaattgtgtcta-atattttgttccatacaatggaaaaactagttcttttcactagttcatatgtc

upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 49
lower sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 12
GGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtgttttgccttaatcaataaatgttttttattgcttttatatatttttacccttatctattaa-tatggtgtttgttaatttaactcccataa-
 || || ||||||||||| ||||||||||||||  | || |||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||    ||| ||||  ||  |     |      ||  | | |||   || ||  |   |  ||     | |   | |   || || |  | ||| || 
TGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattga-atttggcctgtattcacttcagccaaa-atgtcatgtattgtttgttgactggacatagggcctgtttgggtctatacttaagttgccaaaaa

upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 49
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 5'ss of exon 46
GGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtgttttgccttaatcaataaatgttttttattgcttttatatatttttacccttatctattaatatggtgtttgttaatttaactcccataa
 ||||| || |||| ||| ||||||||||||||  | ||| |||||||||||||||| || ||||  |||||||||||||| ||||||||||||||||||||||  | | || |        ||  || | || ||  |||  | |    | |  |     || ||   || ||  |  || | |  |      | | | 
CGTGGAGGACTTCAAAGAATGGACAAATTGGCTCTTTTACAGAGGTGGAATTGGTGTGAAAGGAGCTGAAAGCTGGGAAGCATGGTGGGAAGAAGAACTGgtaagaactattct--------cagaaagttttcttgcttg--tctgagaactaatttttctaacttagaaaataattattat-atctgtgtgtcgacag

upper sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 49
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 44
GGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtgttttgccttaatcaataaatgttttttattgcttttatatatttttacccttatctattaatatggtgtttgttaatttaactcccataa-
 ||||| || ||  | ||||||||||| |||||  | ||| ||||||||||||| |||||||||| |||||||||||| ||||||||||| ||||||||||||  |    |  |    ||||   |   | |   ||  |    |  || |      |  | || | || ||  ||| ||| ||    ||      |  | 
TGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAACTGgtacatctgctcctataataattt-tttgtatagattccttgcatagtagaggaggtcaatcatattttgatcaggttttttttgtaatagtgggaaggac

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|58020049|gb|CX706791.1|CX706791
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGG-GGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|193717024|gb|FK649892.1|FK649892
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|193397230|gb|FK363306.1|FK363306
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|193556241|gb|FK511464.1|FK511464
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|193471075|gb|FK436974.1|FK436974
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAA
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAA
EST: gi|254331761|gb|GR843611.1|GR843611
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAG-AGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|298188356|gb|HO035049.1|HO035049
EST:     TTGGTGTTAAGGAAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|58016476|gb|CX703218.1|CX703218
EST:     GGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: GGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|208259567|gb|GE058421.1|GE058421
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|193448333|gb|FK415914.1|FK415914
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|58019591|gb|CX706333.1|CX706333
EST:     GGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGNAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: GGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|19937309|gb|BQ081239.1|BQ081239
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
EST: gi|58023673|gb|CX710414.1|CX710414
EST:     TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTG                         GCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT
genomic: TTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtg ... tcgtctacagGCTCATATCAGGAGCTTGGGTTCAAGGATAGCAGAAACCATTCTGAGTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGAAGATTTCAGAGATTGGACAAATTGGCTACTCTACCGAGGTGGAATTGGTGTTAAGGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAACTGgtaattagtgttttgccttaatcaataaatgttttttattgcttttatatatttttacccttatctattaatatggtgtttgttaatttaactcccataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC