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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTTGAAGTTGCTTCACTTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagcagtaaatatacaggacggcatttggtttagaaaagagcccattatatttatgctcttccaacatctttccctaatca...

Basic information

species Glycine max
transcript GLYMA14G02880.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02880.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G073743_T03 (Zea mays), 5'ss of exon 3
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTTGAAGTTGCTTCACTTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagcagtaaatatacaggacggcatttggtttagaaaagagcccattatatttatgctcttccaacatctttccctaatca-----
  |||| || || ||  | || || || ||||||||||| || || ||  | |||||||||||||| || || || |||||||||||||| || |||||||||     |  ||||  |  | ||  ||| | |  |||  | || |  | |||  | ||      |  |||           ||||||| |  ||          
AAACTTCGATCCAGTTCGCTACTCTGGTAGATGGTTTGAGGTAGCCTCGTTGAAACGTGGATTTGCTGGTCAGGGACAAGAAGACTGTCACTGTACTCAGgta----ttgtaatacctgaaacatcaaacacattggagaggatatc-tgtagccaggatttttctccattatctaaaaaagaacatctctgtctgtgtgatgat

upper sequence: GLYMA14G02880.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G47860.1 (Arabidopsis thaliana), 5'ss of exon 3
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTTGAAGTTGCTTCACTTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagcagtaaatatacaggacggcatttggtttagaaaagagcccattatatttatgctcttccaacatctttccctaatca
| ||||||||||||| || || || ||||||||||||||||| ||||| ||||| ||||||||||| || |||||||||||||||||||||||||||||||||| || |     || |  |     |||| |     |   |||    |    | |       |  |  |||   || || ||                 
GAACTTTGACCCTGTTAGGTACTCTGGAAGATGGTTTGAAGTAGCTTCTCTTAAGCGTGGATTTGCAGGTCAAGGCCAAGAAGACTGTCATTGCACTCAGgtaattgtttcttcaagtcca----caaat-tgtgaaaacacatcctctgctaacatagtgtgagaacctttcaactgttgcag----------------

upper sequence: GLYMA14G02880.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv19s0177g00320.t01 (Vitis vinifera), 5'ss of exon 3
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTTGAAGTTGCTTCACTTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta-aaataaatatagcagtaaatatac--aggacggcatttggtttagaaaagagcccattatatttatgctcttccaacatctttccctaatca
||| |||||||| || |||||||| ||||||||||||||||| ||||| || |||||||||||||| ||||||||||||||||| || |||||||||||||||||||||    | |  |||    | |  |      ||||   |  |   ||  |    ||   ||  | |   |  ||  |     |||| ||  ||||  
GGATTTTGACCCAGTGAGATATTCTGGAAGATGGTTTGAAGTAGCTTCCCTCAAACGTGGATTTGCTGGACAAGGCCAAGAAGATTGCCATTGCACTCAGgtaaatgctgtggacagttatgattggacctgagatgaggatttctatcctttggggcttgaatgcagaaaaagaaatctggtttctgatctctca-taat--

upper sequence: GLYMA14G02880.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ10882 (Selaginella moellendorffii), 5'ss of exon 1
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTTGAAGTTGCTTCACTTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagcagtaaatatacaggacggcatttggtttagaaaagagcccattatatttatgctcttccaacatctttccctaatca
| ||||||| || |  || ||| | ||  ||||||||||||| || || || || || |||||||| ||||||||||| ||||| || |||||||| || |||| | | ||  |   |    || |     |     ||    ||    ||    | | ||   ||   | |  | || |  ||||              
GAACTTTGATCCCGCCAGGTATGCCGGTCGATGGTTTGAAGTCGCGTCTCTCAAGCGAGGATTTGCCGGACAAGGCCAGGAAGATTGCCATTGCACACAAgtaagttccaagttctct----cattctcgctttgaaactctcttcttcttc---atgggct--tttcgtctgggatcctgtaacag-------------

upper sequence: GLYMA14G02880.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ25927 (Selaginella moellendorffii), 5'ss of exon 1
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTTGAAGTTGCTTCACTTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagcagtaaatatacaggacggcatttggtttagaaaagagcccattatatttatgctcttccaacatctttccctaatca
| ||||||| || |  || ||| | ||  ||||||||||||| || || || || || |||||||| ||||||||||| ||||| || |||||||| || |||| | | ||  |   | | |   |   | |  |   |     ||  |      | | ||   | || |     |   | ||                 
GAACTTTGATCCCGCCAGGTATGCCGGTCGATGGTTTGAAGTCGCGTCTCTCAAGCGAGGATTTGCCGGACAAGGCCAGGAAGATTGCCATTGCACACAAgtaagttccaagttc--tctcgttctcgctttgaaactctcttcttcttc-----atgggcttttcatctgagatcctgtacag----------------

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|151402467|gb|EV272280.1|EV272280
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|298173376|gb|HO016712.1|HO016712
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|192329283|gb|FK020202.1|FK020202
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|151397681|gb|EV267554.1|EV267554
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|192298179|gb|FG991684.1|FG991684
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTCT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|58015930|gb|CX702672.1|CX702672
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|57574781|gb|CX547756.1|CX547756
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT
EST: gi|5760401|gb|AI965692.1|AI965692
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAC                         GGTGTATATACATT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATT
EST: gi|298189122|gb|HO037525.1|HO037525
EST:     TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAG                         GGTGTATATACATTTGATAGGGAAGCACCATCTGTCCAAGTTGATACCTTT
genomic: TTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgcta ... gacatttcagGGTGTATATACATTTGATAGGGAAGCACCATCTATCCAAGTTGATACCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACTTTGACCCTGTAAGATATTCAGGAAGATGGTTTGAAGTTGCTTCACTTAAACGTGGATTTGCGGGACAAGGCCAAGAAGACTGTCATTGCACTCAGgtaaatgctaaaataaatatagcagtaaatatacaggacggcatttggtttagaaaagagcccattatatttatgctcttccaacatctttccctaatca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttccc