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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGATCTCCAAAAATGGGCAACCCACGTAGAGAAGAGAAACCAGCTCCTTATGCTCGGGAAGCAAGAGAATTTCTGAGACAACGACTTATTGGCAAACAGgtattgtgttgagccttttgcattgcctttgtatacgcacatatgaacaagatttgacttcccttttcctgcaacag

Basic information

species Arabidopsis thaliana
transcript AT5G07350.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G07350.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA08G00910.1 (Glycine max), 5'ss of exon 10
CAGATCTCCAAAAATGGGCAACCCACGTAGAGAAGAGAAACCAGCTCCTTATGCTCGGGAAGCAAGAGAATTTCTGAGACAACGACTTATTGGCAAACAGgtattgtgttg-agcct---tttgcattgcctttgtatacgcacatatgaacaagatttgacttcccttttcctgcaacag-------
 || | ||||||| ||||||| || |||||||| || ||||||||||| |||||||| |||||||  || ||  |||||  ||| || |||||    || ||||     |  |   |   | || | || |||    | |   |||  |   |   | | |       |    | || | |       
TAGGTGTCCAAAAGTGGGCAATCCTCGTAGAGATGAAAAACCAGCTCCATATGCTCGCGAAGCAAAGGAGTTCTTGAGAACACGCCTCATTGGTCGTCAAgtatgaaaatataatataaatatgtaatggcttatattgctatcattggtgaatactgttataattaatcgattacacctgttttcag

upper sequence: AT5G07350.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA05G33320.1 (Glycine max), 5'ss of exon 10
CAGATCTCCAAAAATGGGCAACCCACGTAGAGAAGAGAAACCAGCTCCTTATGCTCGGGAAGCAAGAGAATTTCTGAGACAACGACTTATTGGCAAACAGgtattgtg-ttgagcct---tttgcattgcctttgtatacgcacat--atgaacaagatttgacttcccttttcctgcaacag------------
 || | ||||||| | ||||| || |||||||| || ||||||||||| |||||||| |||||||  || ||  |||||  ||| || |||||    || ||||     || |   |   | || | || |||    | |   |||   |||| |   ||  |  |     ||  |  |  |             
TAGGTGTCCAAAAGTAGGCAATCCTCGTAGAGATGAAAAACCAGCTCCATATGCTCGCGAAGCAAAGGAGTTCTTGAGAACACGCCTCATTGGTCGTCAAgtatgaaaatttaatataaatatgtaatggcttatattgctatcattggtgaatacagttatatattataattaatcgattacacctgttttcag

upper sequence: AT5G07350.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA04G38010.1 (Glycine max), 5'ss of exon 10
CAGATCTCCAAAAATGGGCAACCCACGTAGAGAAGAGAAACCAGCTCCTTATGCTCGGGAAGCAAGAGAATTTCTGAGACAACGACTTATTGGCAAACAGgtattgtgttgagccttttgcattgcctttgtatacgcacatatgaacaagatttgacttcccttttcctgcaacag---
 || | ||||||||||||||| || ||| |||| || ||||||||||| ||||| || |||||||  || ||  |||||  ||| || |||||    || ||||       |   | || |||  ||||   |||  ||  | ||||     ||  | ||   |  ||||          
TAGGTGTCCAAAAATGGGCAATCCTCGTCGAGACGAAAAACCAGCTCCCTATGCCCGTGAAGCAAAGGAGTTCTTGAGAACACGCCTCATTGGTCGTCAAgtatga----aaatatcttacat-accttctaatat-catttttgaattcagttgtaattgattactcctatcttttcag

upper sequence: AT5G07350.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA06G17050.3 (Glycine max), 5'ss of exon 10
CAGATCTCCAAAAATGGGCAACCCACGTAGAGAAGAGAAACCAGCTCCTTATGCTCGGGAAGCAAGAGAATTTCTGAGACAACGACTTATTGGCAAACAGgtattgtgttgagccttttgcattgcctttgtatacgcacatatgaacaagatttgacttcccttttcctgcaacag---
 || | ||||||||||||||| || ||| |||| || ||||||||||| ||||| || |||||||  || ||  |||||  ||| || |||||    || ||||     | | | | |   |    ||||  |||  ||  | ||||     ||  | ||   |  ||||          
TAGGTGTCCAAAAATGGGCAATCCCCGTCGAGACGAAAAACCAGCTCCCTATGCCCGTGAAGCAAAGGAGTTCTTGAGAACACGCCTCATTGGTCGTCAAgtatgaaaat-atcttatgataccttcttttaata-acatttttgaattcagttgtaattgattactcctatcttttcag

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|116439364|gb|EG481956.1|EG481956
EST:     ATGCTCGGGAAGCAAGAGAATTTCTGAGACAACGACTTATTGGCAAACAG                         GTTATTGTTCAAATGGAATATTCAAGGAAAGTCACCCAAGGAGATGGTCCT
genomic: ATGCTCGGGAAGCAAGAGAATTTCTGAGACAACGACTTATTGGCAAACAGgtattgtgtt ... cctgcaacagGTTATTGTTCAAATGGAATATTCAAGGAAAGTCACCCAAGGAGATGGTCCT
EST: gi|124729395|gb|EH820797.1|EH820797
EST:     ACAACGACTTATTGGCAAACAG                         GTTATTGTTCAAATGGAATATTCAAGGAAAGTCACCCAAGGAGATGGTCCT
genomic: ACAACGACTTATTGGCAAACAGgtattgtgtt ... cctgcaacagGTTATTGTTCAAATGGAATATTCAAGGAAAGTCACCCAAGGAGATGGTCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGATCTCCAAAAATGGGCAACCCACGTAGAGAAGAGAAACCAGCTCCTTATGCTCGGGAAGCAAGAGAATTTCTGAGACAACGACTTATTGGCAAACAGgtattgtgttgagccttttgcattgcctttgtatacgcacatatgaacaagatttgacttcccttttcctgcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA