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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgttatattaaaatgttgtttataatgcattttacaagatatacaatacaaattgctaatacatgctaatttgtctttataattgctttgcag

Basic information

species Glycine max
transcript GLYMA20G24430.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24430.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os05g43576.1 (Oryza sativa), 5'ss of exon 3
CGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgttatattaaaatgttgtttataatgcattttacaagatatacaatacaaattgctaatacatgctaatttgtctttataattgctttgcag
||| || ||| ||||  | |||||||| ||| | ||||| || |||||||| ||||||||||||||||| || || || || ||| | |||||   |  ||     |  | |  ||    |||     |        | |||   | ||| |  ||    ||  | |                        
CGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAGgtttgtcggtcgccattcagttgtgccactaaattggtggttgtactgtactgaagaaacttttagcttatcttcag-----------------------

upper sequence: GLYMA20G24430.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G101698_T01 (Zea mays), 5'ss of exon 3
CGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgttatattaaaatgttgtttataatgcattttacaagatatacaatacaaattgctaatacatgctaatttgtctttataattgctt-tgcag
     ||||| ||||  |||| ||||| ||| | |||||  | |||||||| |||||| |||||||||||||||| || |||||| | |||||   |   |||| | |     ||  || |       |||   |||  |  |||     |    | |||  ||| ||  || ||   |||| ||| | |||
-----ATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAGgt--ctgccttatctcatgccttttgttgtgccttcctttgttagaatttgaatttgggtaaa-agtactggctgat--gttttctgaattacttcttcag

upper sequence: GLYMA20G24430.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G101698_T02 (Zea mays), 5'ss of exon 3
CGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgttatattaaaatgttgtttataatgcattttacaagatatacaatacaaattgctaatacatgctaatttgtctttataattgctt-tgcag
 || |||||| ||||  |||| ||||| ||| | |||||  | |||||||| |||||| |||||||||||||||| || |||||| | |||||   |   |||| | |     ||  || |       |||   |||  |  |||     |    | |||  ||| ||  || ||   |||| ||| | |||
TGTAGATTATGTTGTGCTAACCAGTGTCGATAGAGATGACTTACCTGATGGTGGAAGTAGCCATTTTGCTCAGACAGTGAAAGCTTTAAAGgt--ctgccttatctcatgccttttgttgtgccttcctttgttagaatttgaatttgggtaaa-agtactggctgat--gttttctgaattacttcttcag

upper sequence: GLYMA20G24430.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G08415.1 (Arabidopsis thaliana), 5'ss of exon 3
CGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttt-tgttatatt---------aaaatgttgtttata-atgcattttacaagatatac--aatacaaattgctaatacatgctaatttg----tctttataattgctttgcag
 || || || || ||  | || || || || ||||| ||| | |||||||| |||||||| |||||||| |||||||||||||||||||||||  ||  | || ||||         |  ||||| ||||   || | ||||     || |    |||     ||   | ||  |   ||  ||    | | |||     || || ||
TGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAGgttattaatattctatttgtttatgcattatgttatttaagcatacctttttgtgcatttctcgaatgttgtttcagagtatttatgaaaatgaaaatatatatctcatctctgtag

upper sequence: GLYMA20G24430.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv10s0071g01020.t01 (Vitis vinifera), 5'ss of exon 3
CGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgttatattaaa-atgttgtttataatgcattttacaagatatacaatacaaattgctaatacatgctaatttgtctttataattgctttgcag
 |||||||| |||||  |||||||||| ||||||||||||||||||||||| ||||||||||||||||||| |||||| || ||||||||||| | | | ||    ||   ||    | ||       | |    | |  ||   | |||      || |  || |  || || | | ||| | ||  ||||
TGTGGATTACATTGTTCTAACAAGTGTTGATCGTGATGATCTGCCTGATGGTGGAAGTGGCCATTTTGCTCGGACTGTTAAGGCTATGAAGgttcatatctttctctagctataaaatctagttactgtgtagttaaaattagggtgcaag--aaaaaaatttgatt-ttagtttctctaactcct--gcag

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|21675910|gb|BQ628261.1|BQ628261
EST:     TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG                         AATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
genomic: TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgt ... tgctttgcagAATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
EST: gi|208082356|gb|GD883890.1|GD883890
EST:     TTGCTCAGACTGTCAAAGCTATGAAG                         AATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
genomic: TTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgt ... tgctttgcagAATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
EST: gi|192312745|gb|FK003971.1|FK003971
EST:     TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG                         AATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
genomic: TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgt ... tgctttgcagAATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
EST: gi|207780441|gb|GD751676.1|GD751676
EST:     TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG                         AATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGG
genomic: TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgt ... tgctttgcagAATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGG
EST: gi|192299138|gb|FG992884.1|FG992884
EST:     TGCCTGATAGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG                         AATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
genomic: TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgt ... tgctttgcagAATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
EST: gi|192312746|gb|FK003972.1|FK003972
EST:     TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG                         AATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT
genomic: TGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgt ... tgctttgcagAATCTCAAACCCGAGATCATGGTTGAGTGTTTAACTTCTGATTTTCGGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAGgtgcttttgttatattaaaatgttgtttataatgcattttacaagatatacaatacaaattgctaatacatgctaatttgtctttataattgctttgcag

- - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA