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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttaccatgagtccatgactactctagagtctaagactaaaacaatttcactaaaaaaactattctccttttctctgcag

Basic information

species Glycine max
transcript GLYMA11G37770.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 13
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 5'ss of exon 12
CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttaccatgagtc-catgactactctagagtctaagactaa--aacaatttcactaaaaa----aactat----tctccttttctctgcag-------
|||||||||||||||||||| ||||| |||||||| |||||  |||| |||   ||||| ||  |||| |  |||||  ||   | | ||    |    |  |||  ||  | |  |  | | |  | |   ||   | | |     ||||||    |   || |    | ||        
CCTGCACATGAGAAGATTGGTGTTGTGGATTCTCAATGGATCATTCATCAAAAGATTCCTTCTTTAGGCAGCCAGgttattaaatgatcaaactttatcttcctatactcaactacattatttactagcttctttgttcatagttttaactatgagatgatctctcaaatacattgatcag

upper sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 13
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 5'ss of exon 13
CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttaccatgagtccatgactactctagagtctaagactaaaacaatttcactaaaaaaact-attctccttttctc--tgcag
||||||||||||||||| ||||| ||||||||||| ||| | ||||| |||  | |||| || || || || || |||  | |     |||    |  |  |||       ||| |    |  |||   ||| || | ||| || |||||  ||  ||   || ||
CCTGCACATGAGAAGATAGGAGTAGTTGATTCTCAATGGGTCGTTCATCAATCTTTTCCTTCCCTTGGCAACCAAgtaaatcc-----catagaactctctctat------gtcca---ttttaacttcttctctcagaaatctgattctttttcgcttgatgtag

upper sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 13
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 5'ss of exon 12
CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttaccatgagtccatgactactcta-gagtctaagactaaaacaatttcactaaaaaaactattctccttttctctgcag---
||||||||||||||||| |||||||| |||||||| |||||  | || |||  | |||| ||  |||| |  |||||    |||| || ||   | |   | | |  ||  ||| |     |      || | | | |   |  | || |  |||||| |  |    
CCTGCACATGAGAAGATAGGAGTTGTGGATTCTCAATGGATCATACATCAATCTCTTCCTTCTTTAGGCAGCCAGgt----tcttgacaataccttctcaatttcagtacaagtattctgttttgttcatat-attgattcagattttttggttttctttttaccag

upper sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv14s0036g00790.t01 (Vitis vinifera), 5'ss of exon 1
-------------------------CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttacc-atgagtccatgactactctagagtctaagactaaaacaatttcactaaaaaaactattctccttttctctgcag--------------------
                         ||||| |||||||| ||||||||||| |||||||| ||||| ||||| |||  | ||||||  || ||||| ||||||  |  | | |  |  | |     |||||  |    | ||  |  ||     | | |  |||| | ||||           ||| ||                    
TGGAACTTCCTCGTCTTTGAAACAACCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCGTTCATCAAACTGTTCCCTTGCTCGGGAACCAGgtaaatcatcttcagaaaaattttctactacatttttatttat-ataaacgttttgtaatgaaaagatctatgaaatagaatactggagtaaccattatgtttttatag

upper sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 8
CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttacc-atgagtccatgactactctagagtctaagactaaaacaatttcactaaaaaaactattctccttttctctgcag--------------------
||||| |||||||| ||||||||||| |||||||| |||||  |||| |||  | ||||||| || ||||| ||||||  |  | | |  |  | |     |||||  |    | ||  |  ||     | | |  |||| | ||||           ||| ||                    
CCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCATTCATCAAACTTTTCCCTCGCTTGGGAACCAGgtaaatcatcttcagaaaaattttctactacatttttatttat-ataaacgttttgtaatgaaaagatctatgaaatagaatactggagtaaccgttatgtttttatag

upper sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv17s0000g02780.t01 (Vitis vinifera), 5'ss of exon 1
-------------------------CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttacc-atgagtccatgactactctagagtctaagactaaaacaatttcactaaaaaaactattctccttttctctgcag--------------------
                         ||||| |||||||| ||||||||||| |||||||| ||||| ||||| |||  | ||||||| || ||||| ||||||  |  | | |  |  | |     |||||  |    | ||  |  ||     | | |  |||| | ||||           ||| ||                    
TGGAACTTCCTCGTCTTTGAAACAACCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAGgtaaataatcttcagaaaaattttctactacattgttatttat-ataaacgttttgtaatgaaaagatctatgaaatagaatactggagtaaccgttatgtttttatag

upper sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 5'ss of exon 4
CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttacc-atgagtccatgactactctagagtctaagactaaaacaatttcactaaaaaaactattctccttttctctgcag--------------------
||||| |||||||| ||||||||||| ||||||||  |||| ||||| |||  | ||||||| || ||||| ||||||  |  | | |  |  | |     |||||  |    | ||  |  ||     | | |  |||| | ||||           ||| ||                    
CCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAAGGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAGgtaaatcatcttcagaaaaattttctactacatttttatttat-ataaacgttttgtaatgaaaagatctatgaaatagaatactggagtaaccgttatgtttttatag

upper sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 13
lower sequence: PP1S70_58V6.2 (Physcomitrella patens), 5'ss of exon 13
CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttaccatgagtccatgactactcta-gagtctaagactaaaacaatttcactaaaaaaactattctccttttc-tctgcag-----------
||||||||||| || ||||||||||| ||| ||||||||||    || |  | | | |  || |||   |    ||| || | ||   ||  |            |||| || |||      |   || ||  | |    |||   |  || || |  | |  ||           
CCTGCACATGATAAAATTGGAGTTGTAGATGCTCAGTGGATCCGACATCGGGTTGTGCTATCTCTAAATAGCTCGgt-ttgtgttcctcacaaccattcactcgttctatgattcttccgagatcgcagttctaatgtcgaaatgctattcgttatggtttatagtaaagcaatat

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|58024808|gb|CX711549.1|CX711549
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctt ... ttctctgcagGGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
EST: gi|51337681|gb|CO981547.1|CO981547
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctt ... ttctctgcagGGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
EST: gi|57574426|gb|CX547401.1|CX547401
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctt ... ttctctgcagGGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
EST: gi|16996411|gb|BM085783.1|BM085783
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctt ... ttctctgcagGGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
EST: gi|192315451|gb|FK009225.1|FK009225
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctt ... ttctctgcagGGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
EST: gi|57574192|gb|CX547167.1|CX547167
EST:     TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG                         GGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG
genomic: TTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctt ... ttctctgcagGGTGAATCTCAAACAGGGAAAGCGCCATGGCAGGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAGgtattttctttaccatgagtccatgactactctagagtctaagactaaaacaatttcactaaaaaaactattctccttttctctgcag

- - - - - - - - - - - - - - - - - AGTGGA