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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTATTTGCCAGTGGAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctctctctctcgttatttctttacccaattcttgttataattataataattattcacactttttttattgcttctttcaaatcccttcacaatt...

Basic information

species Glycine max
transcript GLYMA14G23570.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G23570.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 2
GGTTATTTGCCAGTGGAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgttt---ctctctctctctcgttatttctttacccaattcttgttataattataataattattcacactttttttattgcttctttcaaatcccttcacaatt
        |   |  | ||    |  |  | ||  |||| ||||| ||||||||||  ||||| ||||| ||||| ||||||||||||||||||||||||||      |  |||||||||  |   ||  | |||  ||| |    |  |       |||    |  |  || |     ||||  |  |   ||| |  ||  
CACCGGCGGTGGGCTGGGCAACCTGCGCGCGCTGCTGGCCATCCTCCAGTGGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtccagatttcctctctctccctggatccctcccc--ttccttcctttctctctccgattcaagattccattctcccctcttcaatggatatcctgccaaac-

upper sequence: GLYMA14G23570.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os08g01410.1 (Oryza sativa), 5'ss of exon 1
--GGTTATTTGCCAGTGGAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctctctctctcgttatttctttacccaattcttgttataattataataattattcacactttttttattgcttctttcaaatcccttc-acaatt
   | |    | |  ||   |    |  || |  |  |||| ||||| || |||||||  ||||| ||||| ||||| ||||| ||||| ||||||||||||||| |  |   ||  |  |  || || | |     |                  ||| |||   | ||  ||  |  ||||||    ||| |   |  || 
CAAGATGGGAGACGTTGC--CACCATCCGAGCCGTTCTGGCGATCCTCCAATGGTGGGGCTTCAACGTCACCGTCATCATCATGAACAAATGGATCTTCCAGgttccaattcttccataatc-ttcctctccttttcttcccccccccccccccctattcttcttccgttacttcctttttcttttctgtccttgagatgatc

upper sequence: GLYMA14G23570.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G040033_T01 (Zea mays), 5'ss of exon 1
GGTTATTTGCCAGTGGAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttc-tctctctctctcgttatt-tctttacccaattcttgttataattataataattattcacactttttttattgcttctttcaaatcccttcaca-att-
    ||  |  |  |   |    |  |  |  |  | || ||||| ||||||||||  ||||| ||||| ||||| ||||||||||||||||||||||||||  | || ||| | || | | || | |  | ||   |||| ||    || |  |    |||||   |      || ||    |    |    |  | | ||| 
CAAGATGGGGAACGGCGCCACCATCCGCGCGGTGCTCGCCATCCTCCAGTGGTGGGGATTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtcccgtccctcgcgcttgctcttgtttaaatcctggtcttctt----tttttgtttcaattcaatttccagagatggccatgtatgtagttatatatatattc

upper sequence: GLYMA14G23570.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 1
GGTTATTTGCCAGTG-GAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgttt-ctctctctctctcgttatttctttacccaattcttgttataattataataattattcacactttttttattgcttctttcaaatcccttcacaatt------------------------------------
 |      ||| |   | ||    |  |  |  |  | || ||||| ||||||||||  ||||| ||||| ||||| ||||| |||||||||||||||||||||| | | |  | | |  |   |||   | |||  |   |       | |     | |    |   |  |     ||| ||        ||||   |||                                     
-GGCGCCGGCCGGCCTGGGCACCCTGCGCGCGGTGCTCGCCATCCTCCAGTGGTGGGGCTTCAACGTCACCGTCATCATCATGAACAAGTGGATCTTCCAGgtttacccgcattatattctagcttccccatccatcttccgccgcggatctggatgtcagatgcttctcctgcccggctgctacttttctcctttggaatatctaactaaattcgtccatactgcttaccattatag

upper sequence: GLYMA14G23570.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G127591_T01 (Zea mays), 5'ss of exon 1
GGTTATTTGCCAGTG-GAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgttt-ctctctctctctcgttatttctttacccaattcttgttataattataataattattcacactttttttattgcttctttcaaatcccttcacaatt
 |      ||| |   | ||    |  |  |  |  | || ||||| ||||||||||  ||||| ||||| ||||| ||||| |||||||||||||||||||||| | | |  | | |  |   |||   | |||  |   |       | |     | |    |   |  |     ||| ||        ||||   ||| 
-GGCGCCGGCCGGCCTGGGCACCCTGCGCGCGGTGCTCGCCATCCTCCAGTGGTGGGGCTTCAACGTCACCGTCATCATCATGAACAAGTGGATCTTCCAGgtttacccgcattatattctagcttccccatccatcttccgccgcggatctggatgtcagatgcttctcctgcccggctgctacttttctcctttggaat-

upper sequence: GLYMA14G23570.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G77610.1 (Arabidopsis thaliana), 5'ss of exon 1
GGTTATTTGCCAGTGGAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctctctctctcgttatttc----tttacccaattcttgttataattataataatt--attcacactttttttattgcttctttcaaatcccttcacaatt-----------------------------------------------
  | ||     |  | ||  |||| |||||||| || || || ||||||||||||| ||||||||| || ||||| ||||| ||||| |||||||| |||||||||   |  | || |   |||     |||||  |||| |  |||  |   |  | ||   ||  |    | |  | |||||  |||  |||    |  ||  |                                               
AATCATGGAGGAAGGAAGTATGTTCAGATCTCTATTAGCGATTCTTCAGTGGTGGGGTTTCAATGTTACCGTCATCATCATGAACAAATGGATCTTTCAGgtttcttcttaaccctagaatttttaggttttacttaattgtatttaatacccttttgatctgatctattgatctgatgttgctgatttggaatttggtttcagctttatagattggtgataaagttttgatttttttttgttgttgttgcag

upper sequence: GLYMA14G23570.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv18s0001g02970.t01 (Vitis vinifera), 5'ss of exon 1
GGTTATTTGCCAGTGGAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgttt-ctctctctctctcgttatttctttacccaattcttgttataattataataattattcacactttttttattgcttctttcaaatcccttcacaatt--
  || ||||||||||||||| ||||||||||||  | || |||||||| |||||||  ||||||||||| || |||||||| |||||||||||||| ||||||| || |||   | ||    | ||    |||   ||||       || |   |||   |  || ||  || |||  || ||| |      |||   ||   
TCTTCTTTGCCAGTGGAGCGCGTTTAGATCTCTGCTTGCCATCCTTCAATGGTGGGGGTTCAATGTCACCGTGATTATCATGAACAAGTGGATCTTTCAGgtttgctttctgcttttcagattctcaaatcccccctctttcggcttttgtcg-aatggatttcatttccttaatt--ttgttttattctgtttctggatgtg

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|298164633|gb|HO014278.1|HO014278
EST:     GGTGGGCTTTCAATGTCACTGTCATCATCATCAACAAGTGGATCTTCCAG                         AAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
genomic: GGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctct ... tcttttgcagAAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
EST: gi|298197183|gb|HO041926.1|HO041926
EST:     GGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAG                         AAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
genomic: GGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctct ... tcttttgcagAAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
EST: gi|298180020|gb|HO025235.1|HO025235
EST:     GGTGGGCTTTCAATGTCACCGTCATTATCATCAACAAGTGGATCTTCCAG                         AAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
genomic: GGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctct ... tcttttgcagAAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
EST: gi|193549250|gb|FK507057.1|FK507057
EST:     GGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAG                         AAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
genomic: GGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctct ... tcttttgcagAAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
EST: gi|254349392|gb|GR860190.1|GR860190
EST:     GGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAG                         AAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC
genomic: GGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctct ... tcttttgcagAAATTGGATTTCAAGTTTCCACTGTCGGTATCCTGCATCCACTTCATCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTATTTGCCAGTGGAGCGTGTTTAGATCTCTCTTGGCTATCCTTCAGTGGTGGGCTTTCAATGTCACTGTCATTATCATCAACAAGTGGATCTTCCAGgtttctctctctctctcgttatttctttacccaattcttgttataattataataattattcacactttttttattgcttctttcaaatcccttcacaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc