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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGATCGAGTATCGATGCCATCCGTTTTGGAACCAAAAGTATTGCCCGTCTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaatacaaataatttaactattgatgataagtccatatctattcttttttagcaaattaattgtgtttttttctttctatgttgtgatcatgtag

Basic information

species Arabidopsis thaliana
transcript AT2G39830.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA11G34560.1 (Glycine max), 5'ss of exon 9
CTTGATCGAGTATCGATGCCATCCGTTTTGGAACCAAAAGTATTGCCCGTCTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaatacaaataatt--taactattgatgataagtccata----tctattcttttttagcaaattaattg---tgtttttttctttctatgttgtgatcatgtag---
 ||||| || ||| ||||||| || | ||||||||||||||||||||| ||||| ||||||||||| || ||||| || ||||| || ||| | || |||||| | | ||  | ||||||  ||| | || |    | |   |||    | |  | | | ||     |||   ||   | || |||||||| ||  || |  ||   | |   
TTTGATTGAATATAGATGCCACCCCTATTGGAACCAAAAGTATTGCCCATCTCATGAATATGATAATACAGCTCGGTGCTGTAGTTGTGAAAGATTAGAGgtattaacatg-atataattattaatttttcacaccagggaaataatattttgctatatgttcctccattttctgatcttttattttctttttaaattatcttctccttgaag

upper sequence: AT2G39830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA18G03810.1 (Glycine max), 5'ss of exon 7
CTTGATCGAGTATCGATGCCATCCGTTTTGGAACCAAAAGTATTGCCCGTCTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaata--caaataatttaactattgatgataagtccatatct------attcttttttagcaaattaattgtgtttttttctttctat-gttgtgatcatgtag
 ||||| |||||| ||||||| || | |||||| ||||||||||| || ||||| ||||||||||| || ||||| || ||||| || ||| | || |||||| | | ||   || || | ||   |    |     |    |||| |      || ||| ||        | ||  |   ||||  |||  ||  |  |   | || ||
TTTGATTGAGTATAGATGCCACCCCTATTGGAATCAAAAGTATTGTCCATCTCATGAATATGATAATACAGCTCGCTGCTGTAGTTGTGAAAGATTAGAGgtactaacatgatcacattacttttttcacaacagggaaataatattttgctatatgcttcttcctttttctgatctttcattttcttttaaattatcttctccttgaag

upper sequence: AT2G39830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA14G07060.1 (Glycine max), 5'ss of exon 6
CTTGATCGAGTATCGATGCCATCCGTTTTGGAACCAAAAGTATTGCCCGTCTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaatacaaataattta-actattgatgataagtccatatctattcttttttagcaaat-taattgtgt-ttttttctttctatgttgtgatcatgtag---
 ||||| |||||| | ||||| || ||||||  |||||||||||| || ||||| ||||||||||| || ||||| || ||||| || ||| | ||||||||| |  |||  ||  | |  | ||||||  | ||       |||   |  |||   | ||  | |  || ||  | |  | | ||  |||| || |    | |   
TTTGATTGAGTATAGGTGCCACCCCTTTTGGTCCCAAAAGTATTGTCCATCTCATGAATATGATAATACAGCTCGCTGCTGTAGTTGTGAAAGATTGGAGgtact--aatttaagcactccagactatt--taat-------tattcgtattttcagaacaggtgtttttctgaatctcctttgtcactgttatgtttcccttgaag

upper sequence: AT2G39830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ15933 (Selaginella moellendorffii), 5'ss of exon 6
CTTGATCGAGTATCGATGCCATCCGTTTTGGAACCAAAAGTATTGCCCGTCTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaatacaaataatttaactattgatgataagtccatatctattcttttttagcaaattaattgtgtttttttctttctatgttgtgatcatgtag
| |||| |||||| ||   ||||| ||||||   |||   || || || || || ||| |||| || ||  | ||||||||||||||||| ||||||||||||| |||| |  |||   |   |  ||| |   |  |    ||   || | ||  ||                                           
CCTGATAGAGTATAGAGTTCATCCTTTTTGGGGGCAACGATACTGTCCTTCACATGAAGATGACAACACGCCCCGTTGTTGTAGCTGCGAGCGTTTGGAGgtaagcaaacatgaatcgatctgc-gttgttctcactttgcgat--gttttcttgaag-------------------------------------------

upper sequence: AT2G39830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ33296 (Selaginella moellendorffii), 5'ss of exon 6
CTTGATCGAGTATCGATGCCATCCGTTTTGGAACCAAAAGTATTGCCCGTCTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaatacaaataatttaactattgatgataagtccatatctattcttttttagcaaattaattgtgtttttttctttctatgttgtgatcatgtag
| |||| |||||| ||   ||||| ||||||   |||   || || || || || ||| |||| || ||  | || |||||||||||||| ||||||||||||| |||| |  |||   |   |  ||| |  ||  |    ||   || |  |  ||                                           
CCTGATAGAGTATAGAGTTCATCCTTTTTGGGGGCAACGATACTGTCCTTCACATGAAGATGACAACACGCCCCGATGTTGTAGCTGCGAGCGTTTGGAGgtaagcaaacatgaatcgatctgc-gttgttcttactttgcgat--gttttcctgaag-------------------------------------------

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|116398785|gb|EG441377.1|EG441377
EST:     CTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAG                         TCATGGGATGTGAGATATTACACGTTAGAGGATGGGAGAAGTTTGTGTTTA
genomic: CTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaat ... gatcatgtagTCATGGGATGTGAGATATTACACGTTAGAGGATGGGAGAAGTTTGTGTTTA
EST: gi|116398790|gb|EG441382.1|EG441382
EST:     CTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGGG                         TCATGGGATGTGAGATATTACACGTTAGAGGATGGGAGAAAAGTT-GTGTT
genomic: CTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaat ... gatcatgtagTCATGGGATGTGAGATATTACACGTTAGAGGATGGGAGAA--GTTTGTGTT
EST: gi|116398781|gb|EG441373.1|EG441373
EST:     CTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAG                         TCATGGGATGTGAGATATTACACGTTAGAGGATGGGAGAAGTTTGTGTTTA
genomic: CTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaat ... gatcatgtagTCATGGGATGTGAGATATTACACGTTAGAGGATGGGAGAAGTTTGTGTTTA
EST: gi|116398778|gb|EG441370.1|EG441370
EST:     CTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAG                         TCATGGGATGTGAGATATTACACGTTAGAGGATGGGAGAAGTTTGTGTTTA
genomic: CTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaat ... gatcatgtagTCATGGGATGTGAGATATTACACGTTAGAGGATGGGAGAAGTTTGTGTTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGATCGAGTATCGATGCCATCCGTTTTGGAACCAAAAGTATTGCCCGTCTCACGAATATGATAAAACTGCTCGTTGTTGTAGCTGCGAACGTTTGGAGgtaatcaaatacaaataatttaactattgatgataagtccatatctattcttttttagcaaattaattgtgtttttttctttctatgttgtgatcatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG