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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttgatgttggtctacaatagacatgcttacatgaatatattgtcctatgatttcttttactttttatgggtaacatttcacagtcaagccaag...

Basic information

species Glycine max
transcript GLYMA02G03160.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03160.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os09g22440.1 (Oryza sativa), 5'ss of exon 5
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttgatgttggtctacaatagacatgcttacatga-atatattgtcctatgatttcttttactttttatgggtaacatttcacagtcaagccaag
|| ||  |||| ||||| |||||||| ||  | || ||   ||||||||||||||||||||||||||| || ||||| ||  | ||||||||||| | |    |  |  ||  |   ||    |     | | | | | ||||  |||   ||   |  |  |  | |  |  ||| |||| | |   |  |  
GTGATGGCTGTTATGTCAATGTGGACTAGGTTACAACCGCTTTATGCTGCAAACATGTGGAATGAAGCCCTTAACAAACGACTTGGGACTGAGgtctgtgaacaactctgtgcattgtaatggtttcagctttataaaaattggactacagttctgtgaaactactctttgccacaattcatactttgggtac-

upper sequence: GLYMA02G03160.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G031824_T01 (Zea mays), 5'ss of exon 5
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgt-atatcttgatgttggtctacaatagacatgcttacatgaatatattgtcctatgatttcttttactttttatgggtaacatttcacagtcaagccaag-
|||||  | || ||||| |||||||| ||| ||||||||| ||||||||||||||||||||||||||| || ||||| ||  | || ||||||||  ||  ||  ||||  |    | |   | |  ||   | | |      ||  | ||||  ||| | ||       ||   |  | | |   | ||  |  
GTAATGGCAGTTATGTCAATGTGGACTAGATTGCAGCCAGTTTATGCTGCAAACATGTGGAATGAAGCCCTAAACAAACGACTTGGCACTGAGgttgtagattactgttaatacttattctccctcattgggt-attgggcattcacaagattattttga-ttcaagctagtgtaaggttaaaacaatgctgaat

upper sequence: GLYMA02G03160.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G445478_T01 (Zea mays), 5'ss of exon 5
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttgatgttggtcta--caatagacatgcttacatgaatatattgtc-ctatgatt------tcttttactttttatgggtaacatttca-cagtca--agccaag-------------------------------
|||||  |  | ||||| |||||||| ||| |||||||    |||||| | ||||||||||| |||||||| ||||||||  | ||||||||||||| | |     || || ||    ||   ||| | |   |  || |  |||  ||| ||        |  || |   |   |   ||| |  ||| |  |||   ||  ||                               
GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAGgtatctatatgc-ttagtttagttcattttcatccatttttttatctgctgtttctacgacggaagcattattcaaggtgactaattaaaagctcatcgatcagtggctgaggataccatggcatgcttttgcttggatgtag

upper sequence: GLYMA02G03160.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv01s0026g00920.t01 (Vitis vinifera), 5'ss of exon 5
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtat----atcttgatgttggt-ctacaatagacatgcttacatgaatatattgtcctatgatttcttttactttttatgggtaacatttcacagtcaagccaag
|| ||||||||||||||||||||||| |||||||||||||| ||||||| ||| |||||||||||||| || || ||| || | | ||| |||||||     |  |||  |   |  | || | ||  |  ||   |    |||||||   |  || | | |||       ||| |    | | |  || |       
GTCATTTCTGTCATGTCTATGTGGACTAGAATGCAGCCAGCATATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgttctgaattcaatgtttcagtggat-taattcagtattaatattgttaaaatatatatcttaaaacacttggattttctctaat-gttatctt---

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|9900785|gb|BE609753.1|BE609753
EST:     ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAG                         GATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
genomic: ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttg ... gtgctttcagGATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
EST: gi|207738157|gb|GD715165.1|GD715165
EST:     ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAG                         GATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
genomic: ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttg ... gtgctttcagGATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
EST: gi|192309026|gb|FK001802.1|FK001802
EST:     ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAG                         GATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
genomic: ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttg ... gtgctttcagGATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
EST: gi|192309025|gb|FK001801.1|FK001801
EST:     ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAG                         GATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
genomic: ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttg ... gtgctttcagGATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
EST: gi|298187517|gb|HO034666.1|HO034666
EST:     ATGCTGCAAACATGTGGAATGAAGCGCTGAACAAGCGGTTAGGGACTGAG                         GATTTGGATTTGCACGACATTCTAATTGAGACTGAGAAGCGTGGGATAGCT
genomic: ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttg ... gtgctttcagGATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
EST: gi|6912952|gb|AW394540.1|AW394540
EST:     ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAG                         GATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT
genomic: ATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttg ... gtgctttcagGATTTGGATTTGCATGACATTCTAATTGAGACTGAGAAGCGTGGTATAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtatatcttgatgttggtctacaatagacatgcttacatgaatatattgtcctatgatttcttttactttttatgggtaacatttcacagtcaagccaag

- - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC