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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtacttccactttgattttccatgttttaaataatagatatgacatttttattattattgttttgatgggtatatatatatatatattgctttatc...

Basic information

species Glycine max
transcript GLYMA15G12980.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12980.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 8
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtacttccactttgatttt----ccatgttttaaataatagatatgacatttttattattattgttttgatgggtatatatatatatatattgctttatc
|||||| |||||||| || || ||||||||||| || ||||||| |||||||||||| |||||||| |  ||||||||    |||   |||||||| |||||||||  ||    |||  || |    || || |||   ||| |  ||  | | ||    |||   ||| |   || ||| | ||  ||| || |  | ||   
TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacaccttgcttttggtaa-acctactataattagggtatgcatgtatgattgtgtagacattcata-atttcacattg--

upper sequence: GLYMA15G12980.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 5'ss of exon 6
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaag----tacttcc--------actttgattttccatgttttaaataatagatatgacattttta--ttattattgttttgatgggtatatatatatatatattgctttatc-------------------------------------------------------------------------------
 || || ||| |||||||||||||||| | ||||||| |||||||||| ||||| | ||||||  |||  ||  ||||| | ||||||||| | || ||||||||    ||||||         ||| |   | || || | ||   | ||  ||  || | |   |  |  | ||   || |     |  |  |   ||   | ||||||                                                                                  
GGTGCACTTCCTGGCTTCAAACAATGATTGTGGAGTTCGAGACTTTGACATGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAATgtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacattcaagtcactactgaatgctttgctaaagattcttgcattccatgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcag

upper sequence: GLYMA15G12980.2 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G109039_T04 (Zea mays), 5'ss of exon 2
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtacttccactttgat-----tttccatgttttaaataatagatat---gacatttttattattattgtt-ttgatgggtatatatatatatatattgctttatc
 ||||| |||||||| ||||| || |||||||| || ||| ||| ||| ||||||||||| ||||| |  ||||||||    |||   |||||||| |||||| ||   |    |||  |     ||||  |    | |||  |  ||||   ||  || || ||  |  | || ||    |||| || | | || | ||         
CGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTATGACATGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttctttggtttcttagctatttctgttaccttaatgttctatatttggatcttcttgttggtgctattattacaaggtacatctttctacacat---------

upper sequence: GLYMA15G12980.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv00s1206g00020.t01 (Vitis vinifera), 5'ss of exon 4
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtacttccactttgattttccatgttttaaat-aatagatatgacatttttattattattgttttgatgggtatatatatatatatattgctttatc
   |||||||||||||||||| ||||||| ||||||||| ||||| || |||||||||||||| ||||| |||||||| | ||||||||||||||| |||||||| |  ||    | | |||    |  | | | |  ||    ||   |   |||  ||   || |  | |      ||| ||  ||   ||  | ||  
CACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCAGTGAATgtaagcatctcttactagttttgttgtcatatgagttgattagaattgaagccttaggatagatggtaagctcatgcaataaatccatg-gttcttgtagt

upper sequence: GLYMA15G12980.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv00s0568g00010.t01 (Vitis vinifera), 5'ss of exon 8
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtacttccactttgattttccatgttttaaat-aatagatatgacatttttattattattgttttgatgggtatatatatatatatattgctttatc
   |||||||||||||||||| ||||||| ||||||||| ||||| || |||||||||||||| ||||| |||||||| | ||||||||||||||| |||||||| |  ||    | | |||    |  | | | |  ||    ||   |   |||  ||   || |  | |      ||| ||  ||   ||  | ||  
CACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCAGTGAATgtaagcatctcttactagttttgttgtcatatgagttgattagaattgaagccttaggatagatggtaagctcatgcaataaatccatg-gttcttgta--

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|192303520|gb|FG994498.1|FG994498
EST:     TGGAGAGATTTCAGCTTTCTAAGCATTTCTGCTTTCCTTGGCCAGTAAAT                         CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
genomic: TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtactt ... ctgtctgcagCATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
EST: gi|193462959|gb|FK427724.1|FK427724
EST:     TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAAT                         CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
genomic: TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtactt ... ctgtctgcagCATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
EST: gi|17024037|gb|BM095071.1|BM095071
EST:     TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAAT                         CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
genomic: TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtactt ... ctgtctgcagCATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
EST: gi|58016977|gb|CX703719.1|CX703719
EST:     TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAAT                         CATACTTCATTGAGCCNTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
genomic: TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtactt ... ctgtctgcagCATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
EST: gi|58016661|gb|CX703403.1|CX703403
EST:     TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAAT                         CATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC
genomic: TGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtactt ... ctgtctgcagCATACTTCATTGAGCCCTGATGGGAAACTAGTTGTTATTGTTGGAGACTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtacttccactttgattttccatgttttaaataatagatatgacatttttattattattgttttgatgggtatatatatatatatattgctttatc

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT