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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTAAGAATATTTTAGAAAACCATGCTAGTTACCTGATGTCTGGGAAAGAGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatcttgctgattgacttattctaatcgctgtaagataattttctttttagttttcagtgtttaaattgttcgatgacaccaattgtag

Basic information

species Glycine max
transcript GLYMA18G47050.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47050.1 (Glycine max), 5'ss of exon 19
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 5'ss of exon 18
TGTTAAGAATATTTTAGAAAACCATGCTAGTTACCTGATGTCTGGGAAAGAGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatcttgctgattgacttattctaatcgctgtaagataattttctttttagttttcagtgtttaaattgttcgatgacaccaattgtag
||| | ||||||| | || ||||||||||| ||  |||||||||| || ||||| || ||||| ||||| ||||| |||||||||||||||||| | |||||||||| ||        |||  |  | |||  |   ||     ||  |    |       ||  ||||  | ||  || ||   |  || ||
TGTCATGAATATTCTGGAGAACCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAGCTGGTTGCTTTTGTGAAAGGAACTCAGTTTGATCTTGTGgtaagattttc-------actgttcatcatcattaccagtcttgttgatccaaaaccacatgttattaatatattt-ataacttta--tgcag

upper sequence: GLYMA18G47050.1 (Glycine max), 5'ss of exon 19
lower sequence: AT5G28350.2 (Arabidopsis thaliana), 5'ss of exon 19
TGTTAAGAATATTTTAGAAAACCATGCTAGTTACCTGATGTCTGGGAAAGAGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaag-atcttgctgattgacttattctaatcgctgtaagataattttctttttagttttcagtgtttaaattgttcgatgacaccaattgtag
||| ||||  ||  | ||||  ||||| |||||| |||||||||| ||||| || || |||||||||||||| || ||||| || ||||||||| | |||||| | ||     |  |    ||   ||  ||    |  ||     | |  | ||  | |   |     ||   | | |  |  |||       
TGTAAAGAGCATACTTGAAAGTCATGCCAGTTACTTGATGTCTGGTAAAGAACTTTCAAAGCTTGTTGCATTCGTCAAAGGCACCCAGTTTGATATTGTGgtacgtatacaatttgtacctttcaccttttcatgcttggaaccaatacggtatatatattgattcactaacaataccaaaattccag------

upper sequence: GLYMA18G47050.1 (Glycine max), 5'ss of exon 19
lower sequence: AT3G61480.1 (Arabidopsis thaliana), 5'ss of exon 19
---TGTTAAGAATATTTTAGAAAACCATGCTAGTTACCTGATGTCTGGGAAAGAGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatcttgctgattgacttattctaatcgctgtaagataattttctttttagttttcagtgtttaaattgttcgatgacaccaattgtag
   ||| ||||  ||  | ||||  ||||| |||||| |||||||||| ||||| || || |||||||||||||| || ||||| || ||||||||| | |||||| |    | |   |||    ||||  | |  |  | | |      |  |   || |  |||  || | |    | ||  ||  ||||  ||
TTCTGTAAAGAGCATACTTGAAAGTCATGCCAGTTACTTGATGTCTGGTAAAGAACTTTCAAAGCTTGTTGCATTCGTCAAAGGCACCCAGTTTGATATTgtggtacg--tatacaatttgtaccattc--accttttcatgcttggaaccaataaggtatatagtcattcactaa--caataccaa-aattccag

upper sequence: GLYMA18G47050.1 (Glycine max), 5'ss of exon 19
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 5'ss of exon 19
TGTTAAGAATATTTTAGAAAACCATGCTAGTTACCTGATGTCTGGGAAAGAGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatcttgctgattgacttattctaatcgctgtaagataattttctttttagttttcagtgtttaaattgttcgatgac-accaattgtag
||| || || ||  |||||||||||||||  ||  ||||||| || ||||| || ||||| |||||||||||||| ||||| |||||||||||| |||||||||||             || ||| |  | | | || ||  |||    |  |   |    |  | ||| ||||||     | ||  |||  ||
TGTCAAAAACATCCTAGAAAACCATGCTAACTATTTGATGTCAGGAAAAGAACTTTCCAAACTTGTTGCATTTGTTAAAGGCACTCAGTTTGATCTAGTGgtaagaaaac---------ctcatttt--tggttttaggactattagtatcatcagtggttgcttctaacttgttcaccacctacttattacag

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|12772054|gb|BG236981.1|BG236981
EST:     AGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTG                         GAGTATCTACAACGTGAAAGATATGGAAGTGCTCGGTTGGAGAATTTTGCT
genomic: AGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatctt ... ccaattgtagGAGTATCTACAACGTGAAAGATATGGAAGTGCTCGGTTGGAGAATTTTGCT
EST: gi|11688934|gb|BF596672.1|BF596672
EST:     AGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTG                         GAGTATCTACAACGTGAAAGATATGGAAGTGCTCGGTTGGAGAATTTTGCT
genomic: AGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatctt ... ccaattgtagGAGTATCTACAACGTGAAAGATATGGAAGTGCTCGGTTGGAGAATTTTGCT
EST: gi|22522775|gb|BU081586.1|BU081586
EST:     AGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTG                         GAGTATCTACAACGTGAAAGATATGGAAGTGCTCGGTTGGAGAATTTTGCT
genomic: AGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatctt ... ccaattgtagGAGTATCTACAACGTGAAAGATATGGAAGTGCTCGGTTGGAGAATTTTGCT
EST: gi|13480087|gb|BG509438.1|BG509438
EST:     AGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTG                         GAGTATCTACAACGTGAAAGATATGGAAGTGCTCGGTTGGAGAAATTTTGC
genomic: AGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatctt ... ccaattgtagGAGTATCTACAACGTGAAAGATATGGAAGTGCTCGGTTGGAGAA-TTTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTAAGAATATTTTAGAAAACCATGCTAGTTACCTGATGTCTGGGAAAGAGCTCTCCAAGCTTGTTGCATTTGTAAAAGGAACTCAGTTTGATTTAGTGgtaagatcttgctgattgacttattctaatcgctgtaagataattttctttttagttttcagtgtttaaattgttcgatgacaccaattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA