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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag

Basic information

species Glycine max
transcript GLYMA20G38030.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 5'ss of exon 4
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag-----------------------------------------------------------------------------------------------
 || || || ||||| || ||||||||  | |||||||| ||||| || ||||||||||| ||||||||||||||||||||||| ||  | ||||| |||||    |||  ||  |   |  || || ||| | |     |  |  || |  ||| |    ||| |   || || | | | | |||                                                                                               
AGACACGCTACCTTCAGAATATGATTCACGGGTTAAGGCAATGGAGGTAGATGAAAAGCCTACAGAGGATTACAATGACATTGGTGGCCTTGAGAAACAGgta---tttatttactttaaagatctaatgatgaaaacattagttaggat--ggtcaccattctgtt--gttatgtaagt-agcagtaacttcatttccatatctcataagtgttcatcagttgctgtttgttcattgttatctgctctcttatgttctacttttatattgtctaatgcag

upper sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 4
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagct--ttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag----------------------------------------------------------------------------------------------------
||| || ||||| || |||||||||||  |||| ||||| ||||| || |||||||| || |||||||| |||||||| ||||| ||  | || ||||||||    |  ||  |   ||    || ||     ||   |   ||||||   |      |||||   |        |    |  || ||                                                                                                    
GGACACACTGCCATCAGAGTATGATTCACGAGTAAAGGCAATGGAGGTGGATGAAAAACCCACAGAGGACTACAATGATATTGGAGGTCTTGAAAAGCAGgtacattgcttaataaatgttgaaagttc----agtgttcctttttggaactggaaatattgacaaccatctctttagggaataatagagcaatttgtatcgcttcatgcatcaagcatgttacatttccatccatcttttccttttcataatttatcattctttccatcctattttattgaatatag

upper sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtga---gcttt--ggttcttgccataatttattgaagcac--tttcttttgggggttaggta-attgatctctcaggtcatttcaatcaacag----------
 |||||  ||||||| |||||||| ||  | |||||||| |||||||| ||||| || || || |||||||||||||||||||||||| | ||||| ||||| |   |||||   |  || |   | |  | ||  | ||    | || ||| || || | || ||||    |       | |   ||     |          
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag

upper sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 4
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag--------------
 |||||  |||| || ||||| |||||  |||| ||||| |||||||| ||||||||||| || || ||||| ||||||||||| ||  | || ||||||                                                                                                    
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

upper sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag
||||||| |||| ||||||||||| ||||| ||||| |||||||| || |||||||| ||||| || ||||||||||||||||| ||| |||||||||||||  | ||      |||   |||| |  || |     ||   || |  ||   | || | ||   | || | |||||    |||||
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgttaatctgctgtattgactttgcttcgtagt---gaaactaat---tgagtttatttctgg-aacag

upper sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 4
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactt----tcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag---
 |||||  |||| || |||||||||||| |||| ||||| ||||| ||||||||||| |||||||| || |||||||| || || ||  | ||||||||||  || ||   || |   |||| ||||| ||||   ||      | |  |   || | || ||        |  |    || |   |||    
AGATACTTTGCCATCTGAGTATGATTCTCGAGTAAAGGCTATGGAGGTTGATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttcaattttgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaacttgcctctaattacaacag

upper sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ15061 (Selaginella moellendorffii), 5'ss of exon 4
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag
|||||| || || ||||||||||||||| | || ||||| |||||||| ||||| || || |||||||| |||| ||| ||||| ||  | || || || || |    |   | |     |  ||| || |     ||    |     | | |||  | |                          
GGATACACTTCCGTCCGAGTATGATTCTCGTGTCAAGGCTATGGAAGTCGATGAGAAACCCACAGAGGACTACAGTGATATTGGAGGGCTTGACAAACAAgtaactgcttcatttctttgtgttttcttta-----ttctgatcaaaagcttggtgttag--------------------------

upper sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ37626 (Selaginella moellendorffii), 5'ss of exon 4
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag
|||||| || || ||||||||||||||| | || ||||| |||||||| ||||| || || |||||||| |||| ||| ||||| ||  | || || || || |    |   | |     |  ||| || |     ||    |     | | |||  | |                          
GGATACACTTCCGTCCGAGTATGATTCTCGTGTCAAGGCTATGGAAGTCGATGAGAAACCCACAGAGGACTACAGTGATATTGGAGGGCTTGACAAACAAgtaactgcttcatttctttgtgttttcttta-----ttctgatcaaaagcttggttttag--------------------------

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|208108713|gb|GD907145.1|GD907145
EST:     GGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGG
genomic: GGATTAGAGAAGCAGgtgagctttg ... caatcaacagATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGG
EST: gi|193427383|gb|FK394837.1|FK394837
EST:     CCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGG
genomic: CCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttg ... caatcaacagATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGG
EST: gi|192298921|gb|FG987666.1|FG987666
EST:     TGAAAAGCCAACAGAGGATTACAATGACATTGGGCGGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAAGAGCGG
genomic: TGAAAAGCCAACAGAGGATTACAATGACATTGG-CGGATTAGAGAAGCAGgtgagctttg ... caatcaacagATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGG
EST: gi|192294338|gb|FG987267.1|FG987267
EST:     ATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAAGAGCGG
genomic: ATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttg ... caatcaacagATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGG
EST: gi|208084369|gb|GD882317.1|GD882317
EST:     GGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGG
genomic: GGATTAGAGAAGCAGgtgagctttg ... caatcaacagATTCAAGAATTAGTTGAAGCCATTGTTTTGCCCATGACCCACAAGGAGCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC