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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATTGGTGGAATCAATGGGCTTCTTCATGTCAGTCAGATAAGTCATGACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactcttaaacgtttaatttcagatgttaaaacaacagtccctaacttttaatgtacag

Basic information

species Arabidopsis thaliana
transcript AT5G30510.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 5'ss of exon 4
TGACATTGGTGGAATCAATGGGCTTCTTCATGTCAGTCAGATAAGTCATGACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactcttaaacgtttaatttcagatgttaaaaca---acagtccctaacttttaatgtacag----------------------
 |||||||||||||||||||| ||||| |||||||| ||||| ||||||||||||||  | || ||| | || ||||| || || || || ||  | |||||||  | ||  |    || ||    |   || |  |   | |||   ||    | |    | ||                      
CGACATTGGTGGAATCAATGGCCTTCTCCATGTCAGCCAGATTAGTCATGACCGTGTTGCGGACATCTCGACAGTTCTGCAACCAGGAGATACGCTCAAGgtat-tttttgcattcgtacttgagaaaagtatactatctaaagtttatagagctaaggccagagtattttttttaaatgctattag

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G862107_T01 (Zea mays), 5'ss of exon 4
TGACATTGGTGGAATCAATGGGCTTCTTCATGTCAGTCAGATAAGTCATGACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtat----------actcttaaacgtt------taatttcagatgttaaaacaacagtccctaacttttaatg--tacag
|||||| ||||||||||| || ||||| ||||| || ||||| ||||||||||||||  |||||||| |||| ||||| || || || || ||  | |||||||            ||||    |||      ||     |  |  |  | | |    |  | | || |  ||  || ||
TGACATCGGTGGAATCAACGGCCTTCTCCATGTGAGCCAGATTAGTCATGACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAGgtattgtggctgtggttcttggttgttatgccatatccatacttaatggagctaacaccaatgaattctgttgcttatag

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G03660.1 (Glycine max), 5'ss of exon 4
TGACATTGGTGGAATCAATGGGCTTCTTCATGTCAGTCAGATAAGTCATGACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactcttaaacgtttaatttcagatg---ttaaaacaacagtccctaacttttaatgtacag--------------------
||||||||||||||||| ||| || ||||||||||||||||| |||||||||||| |  | ||||| | |||||||||||| |||||||| | | |||||||| ||   | |     ||  |    ||    ||  ||  ||||    ||  |   ||| || |                     
TGACATTGGTGGAATCAGTGGCCTCCTTCATGTCAGTCAGATCAGTCATGACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATATTCTGAAGgtaaacctatgataagctatgtgagtatttgcttggaatcacagatgttatgtggaaat-taaatctaatttattatttggttag

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G14550.1 (Glycine max), 5'ss of exon 4
TGACATTGGTGGAATCAATGGGCTTCTTCATGTCAGTCAGATAAGTCATGACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctta------------aacgttt------aatttcagatgttaaaacaacagtccctaacttttaatgtacag----
||||||||||||||||| ||| || ||||||||||||||||| |||||||||||| |  | ||||| | |||||||||||| ||||||||   | |||||||| |||  |             |   |||      |||  ||||||| |     |||     |    |||| | |   |    
TGACATTGGTGGAATCAGTGGCCTCCTTCATGTCAGTCAGATCAGTCATGACCGTATAACTGATATTGAAACTGTTCTTCAACCTGGTGATGTTCTGAAGgtaaacttatgctaagctatgccagtatttgcttggaatcacagatgtcatgtggacataaaatcttgtttattatttggttag

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA17G04190.1 (Glycine max), 5'ss of exon 4
TGACATTGGTGGAATCAATGGGCTTCTTCATGTCAGTCAGATAAGTCATGACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctta-------------aacgtttaatttcagatgttaaaacaacagtccctaacttttaat--gtacag
||||||||||||||| ||||| || ||||| || |||||||| ||||||||||||||  | |||||  ||||||| ||||| ||||||||||  || |||||  ||   ||              | ||||   |  |    |  | | || | || | |  || | ||  ||  ||
TGACATTGGTGGAATTAATGGCCTCCTTCACGTTAGTCAGATCAGTCATGACCGTGTAACTGATATTTCAACTGTGCTTCAACCTGGTGACATATTAAAGgttaacctatattaatgttatgtggatgtttgcctagactcttggacataaaaatctcaagtttcttatttgtttag

upper sequence: AT5G30510.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 5'ss of exon 4
TGACATTGGTGGAATCAATGGGCTTCTTCATGTCAGTCAGATAAGTCATGACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactcttaaacgtttaatttcagatgttaaaacaacagtccctaacttttaatgtacag-----------------------------------------
 |||||||||||||| ||||| |||||||||||||||||||| |||||||| |||||||||||||| || || |||||||| ||||||||||   | ||||| | |   |||   | || | |||    |   | |||   ||    |||    |   | |                                          
CGACATTGGTGGAATTAATGGCCTTCTTCATGTCAGTCAGATCAGTCATGATCGTGTCTCAGATATTGCCACAGTTCTTCAACCTGGTGACATCCTCAAGgtttgcctataa---tatactgtcaatactgtcaccaaatttcttccactccctacagataaataaatgtatgtatttattttttgtgtttctcttgctgtag

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|124970854|gb|EL044661.1|EL044661
EST:     ACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAG                         GTTATGATAT-GAGTCACGACCGTGACAG
genomic: ACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAG
EST: gi|125063016|gb|EL131148.1|EL131148
EST:     CAGCCTGGTGACACTTTGAAG                         GTTATGGATATTGAGTACACGACCGTGACAGAGGAAGAGTAAGTCTCTCCA
genomic: CAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTAT-GATATTGAGT-CACGACCGTGACAGAGGAAGAGTAAGTCTCTCCA
EST: gi|86074980|gb|DR370737.1|DR370737
EST:     ACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
genomic: ACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
EST: gi|125153548|gb|EL184640.1|EL184640
EST:     ATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
genomic: ATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
EST: gi|125217781|gb|EL231864.1|EL231864
EST:     ACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGA
genomic: ACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGA
EST: gi|125314161|gb|EL328246.1|EL328246
EST:     TGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
genomic: TGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
EST: gi|47832014|gb|CK121698.1|CK121698
EST:     ACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTG
genomic: ACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTG
EST: gi|124900564|gb|EH975182.1|EH975182
EST:     CAACTGTTCTTCAGCCTGGTGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
genomic: CAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
EST: gi|125033033|gb|EL105302.1|EL105302
EST:     TGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
genomic: TGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
EST: gi|124952318|gb|EL027600.1|EL027600
EST:     ACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
genomic: ACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
EST: gi|124937257|gb|EL014047.1|EL014047
EST:     ATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
genomic: ATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
EST: gi|125212434|gb|EL227388.1|EL227388
EST:     CGCAACTGTTCTTCAGCCTGGTGACACTTTGAAG                         GTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA
genomic: CGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactctt ... taatgtacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACATTGGTGGAATCAATGGGCTTCTTCATGTCAGTCAGATAAGTCATGACCGTGTCTCAGATATCGCAACTGTTCTTCAGCCTGGTGACACTTTGAAGgtatactcttaaacgtttaatttcagatgttaaaacaacagtccctaacttttaatgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG