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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataacacagacaacttgtccatttccaccaagatagttcctagtatcaaacaatgaatgttcttttctatgttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAGACCTAAGAGGCTTAGCGTCAGGATTGAATGGGCAAAACAGTTCAATGAT

Basic information

species Arabidopsis thaliana
transcript AT1G03630.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G03630.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0014g03160.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------gtaaataacacaga-caacttgtccatttccaccaagatagttcctagtatcaaacaatgaatgttctt--ttctatgttcttg--cagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAGACCTAAGAGGCTTAGCGTCAGGATTGAATGGGCAAAACAGTTCAATGAT
                                          || || ||| ||    | ||   | ||| |   | ||   || ||  |    || | | ||| | ||  ||||||    |    |||| ||||||||||| |||||||| ||||| || |||||||| |||||||| ||| | || ||  | ||   |||  | |||||||  ||||| |||   ||
gtactgcaattaatcaggacaaatatgattcatgtaaaatagaagtaccactgaatttcatgatgagttcaatacaaatttgtcatataaatgtactaagtatgctattccttctataaaatgaatcagGGAACACAAATACCTTGGCTGGAAATGTGCCTCCAAAGGCCAACCTTGGGGACTTGAGGGGAATGGCAGGAGGTCTAAATGGGCTGAACAGCTCAGCCAT

upper sequence: AT1G03630.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0059g00270.t01 (Vitis vinifera), 3'ss of exon 3
---------gtaaata-acacagacaacttgtccatttccaccaagatagttcctagtatcaaacaatgaatgttcttt---tcta----tgttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAGACCTAAGAGGCTTAGCGTCAGGATTGAATGGGCAAAACAGTTCAATGAT
         ||| ||  | ||    |||    |||      |  ||| ||||  ||  || || |||   |  |  | |   |||     || | || ||||||||||||| || |||||||| ||||| || |||||||| ||||| || || ||||| ||  | ||   |||||||||||||  |||| | |||   ||
gtggtgtgtgtagatccaaacctctaacaaaaccagaaagccagagagagttgata-cattaagcaagacacatgatctaaatctgcaactgatgtttcagGAAACACAAACACCTTGGCTGGAAATGTGCCCCCAAAGGCTAACCTGGGGGATCTAAGGGGACTTGCTGGAGGATTGAATGGGATAAACGGCTCACCCAT
















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|125302420|gb|EL316505.1|EL316505
EST:     AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAG                         GAAACACAAATACTTT
genomic: AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAGgtaaataaca ... gttcttgcagGAAACACAAATACTTT
EST: gi|125016496|gb|EL088765.1|EL088765
EST:     AATCTGATTATCCATCAAAACGTATGTATCATCGTAGGATCTATAACAG                         GAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG
genomic: AATCTGATTATCCATCAAAACGTATG-ATCATCGTAGGATCTATAACAGgtaaataaca ... gttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG
EST: gi|47830480|gb|CK120164.1|CK120164
EST:     AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAG                         GGAACACAAATACTTTGGCTGGGAATGTACCGCC
genomic: AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAGgtaaataaca ... gttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCC
EST: gi|86060701|gb|DR356458.1|DR356458
EST:     AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAG                         GAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG
genomic: AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAGgtaaataaca ... gttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG
EST: gi|47831169|gb|CK120853.1|CK120853
EST:     AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAG                         GAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG
genomic: AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAGgtaaataaca ... gttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG
EST: gi|124724227|gb|EH815629.1|EH815629
EST:     GTATGATCATCGTAGGATCTATAACTAG                         GAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGA
genomic: GTATGATCATCGTAGGATCTATAAC-AGgtaaataaca ... gttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGA
EST: gi|124838660|gb|EH923099.1|EH923099
EST:     GTATGATCATCGTAGGATCTATAACAG                         GAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG
genomic: GTATGATCATCGTAGGATCTATAACAGgtaaataaca ... gttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG
EST: gi|86030094|gb|DR325847.1|DR325847
EST:     AAAATCTGATTATCCATCAAAACGTATGATCATCGTNNNATCTATAACAG                         GAAACACAAATACTTTGGCTGGGGATGTACCGCCAAAGGCAAACCTTGGAG
genomic: AAAATCTGATTATCCATCAAAACGTATGATCATCGTAGGATCTATAACAGgtaaataaca ... gttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccaagatagttcctagtatcaaacaatgaatgttcttttctatgttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAGACCTAAGAGGCTTAGCGTCAGGATTGAATGGGCAAAACAGTTCAATGAT
                                  ttcttttctatgttct  CT-rich tract
                                     ttttctat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataacacagacaacttgtccatttccaccaagatagttcctagtatcaaacaatgaatgttcttttctatgttcttgcagGAAACACAAATACTTTGGCTGGGAATGTACCGCCAAAGGCAAACCTTGGAGACCTAAGAGGCTTAGCGTCAGGATTGAATGGGCAAAACAGTTCAATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG