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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccccaatgtttttttgtaattttgaatgatcttgaaacagtaattttctgatgtttctctccatcaatcttgtaaaaatagggctgcaaacct...

Basic information

species Glycine max
transcript GLYMA16G26920.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 9
GGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccccaat-gtttttttgtaattttgaatgatcttgaaacagtaattttctgatgtttctctccatcaa-tcttgtaaaaatagggctgcaaacct
 |||||||| || |||||||| ||||| ||| |||| || || ||||||||| | ||||||||||||||||| || |||||||| ||||| ||||||||||||        |||    ||  ||| ||| |    || | |  |    |  |  ||| || |   |  | | ||  |    | |   | ||  |  | ||  
AGGTGGAAACTCAGTGGCTACGGTTGTCTTAAGAGGCAGCACCGATAGTATATTGGATGATCTTGAAAGAGCTGTTGATGATGGTGTGAATACTTACAAGgtatgactgtaaatcaacttcctgtcattgttttggaacataca----tgctactcttatttaattagctaacaggttacctgactgttggtgtttatacag

upper sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 9
GGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccccaatgtttttttgtaattttgaatgatcttgaaacagtaattttctgatgtttctctccatcaatcttgtaaaaatagggctgcaaacct-
 ||||||||||| |||||||||||||| ||  |||| |||||||| |||||||||||||||||||||||||| || |||||||| || || || ||||||||| | |     |  | |      | | ||  ||  | ||| |||  |   | |||| | |     || ||     || | |   |     |  |  |   
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgta-tctatagtacatgtgacctaactcttttattgtattgtaacgttctgtgtctgttttgctaatctattcgagttctcactgtccttgtttattctag

upper sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 9
GGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttcccca-atgt--------ttttttgtaattttgaatgatcttgaaacagtaattttctgatgtttc----tctccatcaatcttgtaaaaatagggctgcaaacct
 ||||||||||| |||||||||||||| ||  |||| |||||||| |||||||||||||||||||||||||| || |||||||| || || || |||||||||  |     | ||||        | |||| |  | ||| |   |  ||   | ||  ||| || || | |     |   ||     |||||  |     | |      |  
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatagtacatgtgacctaactcttttattgtattgtaacgttctgtgtctgt--tttgctaatctattcgagttctcactgtccttgtttattctagtcaatgtgcag

upper sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G381744_T01 (Zea mays), 5'ss of exon 9
GGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccccaatgtttttttgtaattttgaatgatcttgaaacagtaattttctgatgtttctctccatcaatcttgtaaaaatagggctgcaaacct------------
 ||||||||||| ||||||||||||||  |  |||| |||||||| |||||||||||||||||||||||||| || |||||||| || || || |||| |||| | ||     | | | |     ||      | ||  |      |||   || | |  |   | ||  |  | ||  |  |   | |    ||    |            
TGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACATACAGGgta-tgtctgtggtatctataatagatgcgacctaattcttttgttgta---ttgtaacatccatgtctgtttagctaatctatccaagttctcactgtttttttatactag

upper sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 9
GGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccccaatgttt-------ttttgtaa-------ttttgaatgatcttgaaacagtaattttctgatgtttctctccatc-----aatcttgtaaaaatagggctgcaaacct----------------
 |||||||| || ||    ||||| ||||||||||||||||||||||||||| ||||||| |||||||||||||| ||||| || ||||| || |||||||||| ||    | ||  |       | ||||||       ||||  |  |   || |   ||  ||   | || | |  ||   |      ||  || | |   ||    |     | |                
AGGTGGAAACTCCGTATGCACTGTGGTTTTACGAGGAAGTACTGATAGTATATTAGATGACCTTGAAAGAGCAGTTGATGACGGTGTGAATACATACAAGgtaaattttatattggatgggctggtcttgtaaatataggtttttgagcactatggagtggtggttgcatcatctcttacttttttgttggaaatttatgacgttaatattaggtgctttacatttcaatgccag

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|58024895|gb|CX711636.1|CX711636
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccc ... tatttgtcagGCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
EST: gi|7234248|gb|AW569587.1|AW569587
EST:     GATGATGGAGTGAACACTTACAAG                         GCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
genomic: GATGATGGAGTGAACACTTACAAGgtaatttccc ... tatttgtcagGCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
EST: gi|213599562|gb|DB962765.1|DB962765
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccc ... tatttgtcagGCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACT
EST: gi|192332268|gb|FK023917.1|FK023917
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccc ... tatttgtcagGCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
EST: gi|193649445|gb|FK597912.1|FK597912
EST:     AACACTTACAAG                         GCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
genomic: AACACTTACAAGgtaatttccc ... tatttgtcagGCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
EST: gi|31467884|gb|CD409912.1|CD409912
EST:     GGATGATGGAGTGAACACTTACAAG                         GCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
genomic: GGATGATGGAGTGAACACTTACAAGgtaatttccc ... tatttgtcagGCCATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCAACTGAAATT
EST: gi|26268510|gb|CA819573.1|CA819573
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCCATGTGCAGGGATAGCCGCTTTGTACCTGG
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccc ... tatttgtcagGCCATGTGCAGGGATAGCCGCTTTGTACCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccccaatgtttttttgtaattttgaatgatcttgaaacagtaattttctgatgtttctctccatcaatcttgtaaaaatagggctgcaaacct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctctcc