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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGCCTGAAACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaagaatcttggtggatcatgttgattagtgtgtaatgtagaactgttgtaaaagtgagaaatattaatgcagaattgctgatgatcatgcaact...

Basic information

species Glycine max
transcript GLYMA19G24250.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 2
TGTGCCTGAAACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaagaatcttggtg-gatcatgttgattagtgtgtaatgtagaactgttgtaaaagtgagaaatattaatgc--agaattgctgatgatcatgcaact
|    | ||    || |  ||||| |||||||| ||||| |||||||| || |||||||||||||| ||||| || || || | ||| || |    |||||||   |  | |||   |   ||  |     |||| || |||  |  ||||||  |  |  |          ||| |  || |  | ||   |||||   |  
TCCTTCAGAGCAAGGTTGTCTCTCCATTGTTGTACTTGGGGCTTCTGGTGACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaactattctctatacaattttacaacttagagtataacttc-aactgtaatgcacatttttttctcaaatacacaggagagttgcacatcattaca--

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 2
TGTGCCTGAAACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaagaatcttggtggatcatgttgattagtgtgtaatgtagaactgttgtaaaagtgagaaatattaatgcagaattg---ctgatgatcatgcaact--
     | ||  |||| |   | || |||||||| || ||||||||||| || |||||||||||||| || || || || || || || || | || ||||||||   |  |||      | |  |||   ||| | | ||| |     ||      | ||    | | |  |||||| | ||    |      |  |     |  
ATCTTCAGAGTCTGGCTGCTTGTCCATTGTTGTACTAGGCGCTTCTGGAGACCTTGCTAAGAAGAAAACTTTCCCAGCGCTCTTTCACCTTTTCCAGCAGgtaagttaatatcactagcggttttgt-acttaatatataaagc----cttcaaacagagaattacaaacaaatgcatagtttgatccatctcttctttggttat

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTGCCTGAAACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaagaatcttggtggatcatgttgattagtgtgtaatgtagaactgttgtaaaagtgagaaatattaat-gcagaattgctgatgatcatgcaact---
 || || |||||||| |  || || ||  | || ||||| |||||||| |||||||||||||||||||| |||||||| |||||  |  ||||||| |||||           ||| |  || ||      | |||  |    |||||    |      || |    | ||| |    |  ||  || |    |||    |   
AGTTCCAGAAACTGGTTGTCTTTCAATCATAGTTCTTGGTGCTTCTGGTGATCTTGCTAAGAAGAAGACTTTTCCTGCTCTTTTTAACTTATACCGTCAGgt-----------ttgttccat-atcagagctggtgcatgtgttagaatcaatcctctggttaattgtgttagttatggtttttttggtttgtatgatggtcag

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 5'ss of exon 3
TGTGCCTGAAACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgt----------aaagaagaatcttggtggatcatgttgattagtgtgtaatgtagaactgttgtaaaagtgagaaatattaatgcagaattgctgatgatcatgcaact
 ||  | |||||||||   ||||||||  |||| ||||| |||||||| |||||||||||||||||||| ||||||||||||||| ||||||  |  |||||          ||| |||||||||  |     || ||   | || |  |||||       || ||    |  ||  | || ||   |  || |  |||| ||       
AGTCACGGAAACTGGGAGTCTCTCTATCATTGTTCTTGGTGCTTCTGGTGATCTTGCTAAGAAGAAGACTTTTCCTGCACTTTTCAATCTATTTCATCAGgtttttttaaacaaacaagaatcttttt----tatcttttattgttttcaatgtcacttgtttttatttatttgatgtgtttat-tggttttac--atgagcacag----

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 2
TGTGCCTGAAACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaagaat--cttggtggatcatgttgattagtgtg-taatgtagaactgtt--gtaaaagtgagaaatattaatgcagaattgctgatgatcatgcaact
 ||||| ||||||||||  ||||||||| |||||||||| ||||| || |||||||| ||||||||||| ||||| || || ||| | || ||||| |||||      |  |  |||| ||  || |||  || | | || |  | | |     ||  || |   | |  |   |||||  | ||   || |     || ||   
CGTGCCGGAAACTGGGTGTCTCTCTATTATTGTGCTTGGTGCTTCCGGTGATCTTGCCAAGAAGAAGACTTTTCCAGCTCTCTTCAACCTTTACCGCCAGgtttgacgggcttgcttgctgtgtcttgtatataaatttgatgttcttgtgtgatttggttatgatcattagggttaatataaaa--actaaaatcaatcca---

upper sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S73_244V6.3 (Physcomitrella patens), 5'ss of exon 2
TGTGCCTGAA-ACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaagaatcttggtggatcatgttgattagtgtgtaatgtagaactgttgtaaaagtgagaaatattaatgcagaattgctgatgatcatgcaact-----
   |  |||  |||||||  ||||||||||| ||||| || || ||||| |||||||| ||||||||||| ||||| ||  ||||| | || |||  ||||||| | | |   ||     ||     ||  |  || | | |   |   ||  | |  | ||  ||  |  |     |   | | || | |  | |    |     
-AAGTGTGATTACTGGGTACCTCTCTATTGTCGTGCTGGGTGCATCTGGAGATCTTGCGAAGAAGAAGACTTTTCCAGCCATTTTCAACCTTTACACGCAGgtaca-atgttactcacccgact---ttcgtgtgtatcttaatcacctctcgtttggaggtt-gacgtggtctcagactctcggtgtttacgacgagctttgtgt

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|254334914|gb|GR844699.1|GR844699
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAG                         GGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaaga ... ctattttcagGGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
EST: gi|192294272|gb|FG986361.1|FG986361
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAG                         GGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaaga ... ctattttcagGGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
EST: gi|213594579|gb|DB957998.1|DB957998
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAG                         GGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaaga ... ctattttcagGGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
EST: gi|298180491|gb|HO022044.1|HO022044
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAG                         GGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaaga ... ctattttcagGGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
EST: gi|298167590|gb|HO012853.1|HO012853
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAG                         GGATTCTTACCAGCAGATGAAGTTCACATTTT-GGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaaga ... ctattttcagGGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
EST: gi|213611006|gb|DB970933.1|DB970933
EST:     ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAG                         GGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA
genomic: ATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaaga ... ctattttcagGGATTCTTACCAGCAGATGAAGTTCACATTTTTGGCTATGCAAGGACAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGCCTGAAACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaagaatcttggtggatcatgttgattagtgtgtaatgtagaactgttgtaaaagtgagaaatattaatgcagaattgctgatgatcatgcaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggtgg