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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATTTCTTTTCTCATTTGGAGATGCATATGAGGCAGGATCACCCACCTTTGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctagtcaatattatgttgtttgttctttctattcagttattggaaagcattatttgctatctatatgataagagcatcttccctgttatatttt...

Basic information

species Glycine max
transcript GLYMA20G38460.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38460.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g04480.1 (Oryza sativa), 5'ss of exon 2
TGATTTCTTTTCTCATTTGGAGATGCATATGAGGCAGGATCACCCACCTTTGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgt-atacctagtcaatattatgttgtttgttctttctattcagttattggaaagcattatttgctatctatatgataagagcatcttccctgttatatttt-------------------------------------------------------------------------------
||| ||||||||||| |||||||||||| |  | ||||| || ||||| || ||||||||||| |||||||| || |||||||| |||||||| || ||||| |||  |  |   | || | | | ||      | | | ||   |    | |  |||||     ||  ||||  | | | | | ||  |   | | |                                                                                  
TGACTTCTTTTCTCACTTGGAGATGCATCTCCGCCAGGAGCATCCACCATTATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatattattttttttgtttagattagctagtatgt-caaccaacacaga-tattatcacaaatgcatatatttataacttttttaccactttgtcggatagaatatccaggtgtaaaggcagttggcagtatctgttttatgtttgatgatggagtttcgttttggtttgtttcag

upper sequence: GLYMA20G38460.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G096972_T01 (Zea mays), 5'ss of exon 2
TGATTTCTTTTCTCATTTGGAGATGCATATGAGGCAGGATCACCCACCTTTGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctagtcaatattatgttgtttgttctttctattcagttattggaaagcattatttgctatctatatgataagagcatc--ttccctgttatatttt------
||||||||| ||||| |||||||||||| || | ||||| || ||||| |||||||||||||| |||||||| || ||||||||||||||||| || |||||| |        || ||   |   |||   ||  ||  |||    |  | |  | | |        |||   | ||   || |   | |   |||| ||        
TGATTTCTTCTCTCACTTGGAGATGCATCTGCGTCAGGAGCATCCACCATTGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaa--------atgttccttgaattggatttgttaaccaggcgatatataatactctgattctaatattctacaatgtcaccaagtgcacattatgttagcatgag

upper sequence: GLYMA20G38460.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G55200.1 (Arabidopsis thaliana), 5'ss of exon 2
TGATTTCTTTTCTCATTTGGAGATGCATATGAGGCAGGATCACCCACCTTTGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctagtcaatattatgttgtttgttctttctattcagttattggaaagcattatttgctatctatatgataagagcatcttccctgttatatttt
 |||||||| |||||| |||||||||| |||||||||||  | || ||| | || || |||||||||||||| || |||||||| |||||||| || ||||||     |  ||| |     ||| || ||| | | | |||   |  | |   | ||  ||   |  |  |   |    |||||||    || | |    
GGATTTCTTCTCTCATCTGGAGATGCACATGAGGCAGGAGTATCCTCCTCTCTGCGGGAGAGACCACATGGCTTACAGATCTGCATATTTTCCGGTCAAGgtaa--taaaccaaaacccatttgctt-ttcctccaaatca---aaagaagtcccttgattttgaatttgacactttttgcatctt----gtaacag---

upper sequence: GLYMA20G38460.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv00s0317g00100.t01 (Vitis vinifera), 5'ss of exon 2
TGATTTCTTTTCTCATTTGGAGATGCATATGAGGCAGGATCACCCACCTTTGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctagtcaatattatgttgtttgttctt-tctattcagttattggaaagcattatttgctatctatatgataagagcatcttccctgttatatttt----
||| ||||||||||| ||||||||||||||||| ||||| ||||||||| ||||||||||||| |||||||| || |||||||| |||||||||||||||||  ||    ||  |  |   ||||    ||   |  |  || || |   |  ||   | |  | ||  |  |  ||  |   || |   | || | ||||    
TGACTTCTTTTCTCACTTGGAGATGCATATGAGACAGGAACACCCACCTCTGTGTGGAAGAGATCACATGGCTTACAGATCTGCTTATTTTCCTGTTAAGgtgaac----tctttgcttcattgtcccctcaaatgcacacatttttcacattgc-caagtcaccatagacctactataaatttcattatttttctcttttctct

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|208299552|gb|GE097105.1|GE097105
EST:     TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTCTCCTGTTAAG                         GATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
genomic: TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctag ... tattgtgtagGATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
EST: gi|151393848|gb|EV263723.1|EV263723
EST:     TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAG                         GATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
genomic: TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctag ... tattgtgtagGATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
EST: gi|192334350|gb|FK024421.1|FK024421
EST:     TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAG                         GATGTTATTGATGGGGATCTATGTGAGCAATACCCAACATTGCCAATGGAT
genomic: TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctag ... tattgtgtagGATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
EST: gi|193408140|gb|FK375350.1|FK375350
EST:     TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAG                         GATGTTATTGATGGGGATCTATGTGAGCAATACCCAACATTGCCAATGGAT
genomic: TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctag ... tattgtgtagGATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
EST: gi|254324564|gb|GR833989.1|GR833989
EST:     TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAG                         GATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
genomic: TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctag ... tattgtgtagGATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
EST: gi|193542645|gb|FK501054.1|FK501054
EST:     TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAG                         GATGTTATTGATGGGGATCTATGTGAGCAATACCCAACATTGCCAATGGAT
genomic: TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctag ... tattgtgtagGATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT
EST: gi|208119365|gb|GD914232.1|GD914232
EST:     TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAG                         GATGTTATTGATGGGGATCTATGTGAGCAATACCCAACATTGCCAATGGAT
genomic: TGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctag ... tattgtgtagGATGTTATTGATGGGGATCTATGCGAGCAATACCCAACATTGCCAATGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATTTCTTTTCTCATTTGGAGATGCATATGAGGCAGGATCACCCACCTTTGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctagtcaatattatgttgtttgttctttctattcagttattggaaagcattatttgctatctatatgataagagcatcttccctgttatatttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA