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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatatactacacgatttttagagcttttttttaatggcaatatcaagcagtaacatgtccgtatgcatatcatagtttctccctctgaaaatactc...

Basic information

species Glycine max
transcript GLYMA16G32990.1
intron # 4
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 4
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 4
GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatatactacacgatttttagagcttttttttaatggcaatatcaagcagtaacatgtccgt---atgcatatcatagt-ttctccctctgaaaatactc
||||||||||| ||||| || || || |||||||| ||||||||||| || || |||||| ||||||| || |  ||||||||||| || ||||||||||   |   ||| | |    |   |  | |||  || ||   |   |           | || ||    || ||  |  | | || || |   |  || ||  
GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgccctatatg----tcgtacttctttcatagtgtacagtccggaggaccttttctcggtttattggatgccgcaatgttttctcgaagtcaaaacct

upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 3
GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatatactacacgatttttagagcttttttttaatggcaatatcaagcagtaacatgtccgt--atgcatatcatagtttctccctctgaaaatactc
||||||| ||| ||||| || || || |||||||| |||||||||||||| || |||||  ||||||| |||||||||||||| || || |||||||||| |||    |    |    |  |||   |   |  | ||  ||| ||    || | ||||      |    |  | |  | |       |  |||   ||
GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccatttctgtacatgtgagaactgcctcca-ggttata-cagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc

upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G51570.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatatactacacgatttttagagcttttttttaatggcaatatcaagcagtaacatgtccgtatgcatatcatagtttctccctctgaaaatactc--
|||||||| |  |||||||| || || |||||||| || |||||||| ||||| ||||||||  |||| || ||||||||||| || ||||||||||||||  | || | | ||||  | || |  |   | |  ||  | | |  ||   |   |||      | || |||| ||          |  | | | |   
GTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAGgtaacctttatttc-cgatactgagggaatcagtgtc-tgatacttttcaggtctctaatggttccctacacatcaaagcacagaaagatttatacatttta

upper sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv16s0022g01690.t01 (Vitis vinifera), 5'ss of exon 4
GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaat-atatactacacgatttttagagcttttttt-taat--ggcaatatcaagcagtaacatgtccg-tatgcatatcatagtttctccctctgaaaatactc
||||||||||  || |||||||  |||||||||||||| ||||||||||||||||||||| || |||| || ||||||||||||||||| |||||||||  | |  | ||||    |||||   | | || ||  ||   | |||  |    || | | |  |||  | |   ||  || | || ||  | |  | |     
GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGgttttgaccttctactgtttttttcttgttcttattgcaactggacaaattttctcattcaaacttccaatgtaggtagaatggattttcaatatccaga-----

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|254327495|gb|GR837050.1|GR837050
EST:     TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG                         CTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
genomic: TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatata ... tattttacagCTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
EST: gi|254346709|gb|GR856431.1|GR856431
EST:     TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG                         CTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
genomic: TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatata ... tattttacagCTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
EST: gi|192328203|gb|FK022882.1|FK022882
EST:     TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG                         CTCAAAGGATGCAA
genomic: TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatata ... tattttacagCTCAAAGGATGCAA
EST: gi|254323382|gb|GR835883.1|GR835883
EST:     TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG                         CTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
genomic: TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatata ... tattttacagCTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
EST: gi|51345167|gb|CO985900.1|CO985900
EST:     TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG                         CTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
genomic: TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatata ... tattttacagCTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
EST: gi|209701321|gb|BW655916.1|BW655916
EST:     TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG                         CTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
genomic: TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatata ... tattttacagCTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
EST: gi|298184948|gb|HO030161.1|HO030161
EST:     TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG                         CTCAAAGGATGCAACTTGCTAGTCAG
genomic: TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatata ... tattttacagCTCAAAGGATGCAACTTGCTAGTCAG
EST: gi|120530546|gb|EH258679.1|EH258679
EST:     TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG                         CTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT
genomic: TATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatata ... tattttacagCTCAAAGGATGCAACTTGCTAGTCAGTACAAAGGAGAAGCTGAAAAGATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatatactacacgatttttagagcttttttttaatggcaatatcaagcagtaacatgtccgtatgcatatcatagtttctccctctgaaaatactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctc