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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATGAAACTACTTTATCCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttactttcttccttcaccttaactttttttttttttttttttatcttatacaaaccatcaaaccattacaattcctatttcctcaccctgcatt...

Basic information

species Glycine max
transcript GLYMA13G44910.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44910.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
GCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATGAAACTACTTTATCCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgta---cctttactttcttccttcaccttaactttttttttttttttttttatcttatacaaaccatcaaaccattacaattcctatttcctcaccctgcatt
 || ||||| ||||||||||| ||||||||||||||||||| ||| ||    || || || |||  ||| | ||| ||| | |||||||||||||||||||||   |   ||  | ||   |  |  |||| |  |  | || ||| ||     | ||  ||  | |      | |  |       | |       | |||  
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataatttaaatggtgatgttatttattacgcttcatttaattcttttc-tgactggatgctgggtgtaacggtgcagca--

upper sequence: GLYMA13G44910.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G143462_T06 (Zea mays), 5'ss of exon 2
GCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATGAAACTACTTTATCCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgt--acctttactttcttccttcaccttaactttttttttttttttttttatcttatacaaaccatcaaaccattacaattcctatttcctcaccctgcatt
 ||| |||| |||  |||||| ||||| ||||||||||||| ||| ||    || ||||| |||  ||||||||| ||||| ||||||||||||||||||||     | || |   |  ||  ||   | | ||||    |   | |  | | |||    ||  ||    |  ||     |  || |    |  | ||  ||
ACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATGAAAGTACATTGGAAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttctaatacatctctgtactaca-cattttcagatagatatgatgttttac-tgaagtatttttcattttagtctgataatgttaccacttgattt

upper sequence: GLYMA13G44910.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G79650.1 (Arabidopsis thaliana), 5'ss of exon 2
GCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATGAAACTACTTTATCCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttactt-tcttccttcaccttaactttttttttttttttttttatcttatacaaaccatcaaaccattacaattcctatttcctcaccctgcatt
||||||| | ||||||||||| || |||||||||||||||||||   |    || || || ||  | ||||| || ||||| || || |||||||| |||||| |  | |   |||  || |  |  |  |  |  || |||| | || | |  || ||  |     |   |    ||       |         || || 
GCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATGAAACTAGCCTGGTGGAGAACAAAGTTACGGAGGAAGGATTTCTCGTCGTTATGCTTAGCAAGgtaacagttcaaatctggctactgcaaagatcatacttcttttatcttcaacaaat-cagtcttcttatttaccttaaacaaggataaaagctgatgaata

upper sequence: GLYMA13G44910.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 5'ss of exon 2
GCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATGAAACTACTTTATCCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacct--ttactttcttccttcaccttaactttttttttttttttttttatcttatacaaaccatcaaaccat-tacaattcctatttcctcaccctgcatt
|||||| || ||||||||||| ||||||||||||||||||||||| ||    || || |||||  | ||||| ||||||||||| || |||||||| |||||||||   |  ||||||   | | | ||  |  |  ||  | |   |  |   ||  |||  | |  |   || ||   ||| || | ||      |  | |
GCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATGAAACTACCTTGGTGGAGAACAAGGTTACCGAGGAGGGTTTTCTTGTCGTGATGCTTAGCAAGgtacctatctgatttcttttatgatcctagatagtgcttagtgtgagtc-actctaagcaa--cctggatttatatatccttcttagtcccattagatatagt

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|192315478|gb|FK007796.1|FK007796
EST:     CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAG                         GGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
genomic: CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttac ... tcatttgcagGGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
EST: gi|298173138|gb|HO020122.1|HO020122
EST:     CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAG                         GGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
genomic: CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttac ... tcatttgcagGGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
EST: gi|192315477|gb|FK007795.1|FK007795
EST:     CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAG                         GGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
genomic: CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttac ... tcatttgcagGGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
EST: gi|298191541|gb|HO039020.1|HO039020
EST:     CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAG                         GGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
genomic: CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttac ... tcatttgcagGGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
EST: gi|193323635|gb|FK290487.1|FK290487
EST:     CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAG                         GGTAAAACCTTGGGATCTGCTGGCATTTCA
genomic: CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttac ... tcatttgcagGGTAAAACCTTGGGATCTGCTGGCATTTCA
EST: gi|192307602|gb|FG999641.1|FG999641
EST:     CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAG                         GGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG
genomic: CCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttac ... tcatttgcagGGTAAAACCTTGGGATCTGCTGGCATTTCATCAACTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATGAAACTACTTTATCCGACAATAAGGTCTCTGAGGATGGTTTTCTTGTTGTCATGCTTAGTAAGgtacctttactttcttccttcaccttaactttttttttttttttttttatcttatacaaaccatcaaaccattacaattcctatttcctcaccctgcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaccc