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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggatcaccaagtagagctgaaattaagggtgtctgatcaccaatacatgtggcttgtctagtctttattaccaaatcatcagaagcatttatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGTTAAGTTGGGAGCAGATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTC

Basic information

species Arabidopsis thaliana
transcript AT1G15370.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15370.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 1
-gggatcaccaagtagagctgaa--attaagggtgtctgatcaccaatacatgtggcttgtctagtctttattaccaaatcatcagaagcat-ttatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGTTAAGTTGGGAGCAGATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTC
  | || |   | |||   ||    |  || |    ||||     |  |  | |||   |  |    |  |||||  | | |  ||    ||  | | |||||| || | |||||| ||||| || |||||||| || ||| |||||||||||||||| |||||||| || ||||| |||||||| ||||||||||||||||| 
atgaatgaatgaatagctttgcttcagaaatgactgctgaatttgatcatgtatggtaagattg--ttgaattactgattta--aggtttatgctgtattgcagATTTAGTGGAGTCCCAGCAGAAGAACGGCTGCATTGGAGATCTTTCTTGGTTAAATTGGGAGCGGACAATCTTAAAGGCGTAAAAAATGAGGAGCTTCTT
















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|86081993|gb|DR377752.1|DR377752
EST:     ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAG                         GTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT
genomic: ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAGgttcgtactt ... tatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT
EST: gi|164112283|gb|ES024827.1|ES024827
EST:     ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAG                         GTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGC
genomic: ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAGgttcgtactt ... tatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGC
EST: gi|152035004|gb|BP841901.2|BP841901
EST:     ATCCTAGCTGTGTTGTTCGCCAATTCCGTGGGGAATGTTTTAATCGAAAG                         GTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT
genomic: ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAGgttcgtactt ... tatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT
EST: gi|116437502|gb|EG480094.1|EG480094
EST:     ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAG                         GTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT
genomic: ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAGgttcgtactt ... tatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT
EST: gi|125031619|gb|EL103888.1|EL103888
EST:     CTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAG                         GTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGGTCTTTCTTGGT
genomic: CTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAGgttcgtactt ... tatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT
EST: gi|152035520|gb|BP856874.2|BP856874
EST:     ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAG                         GTT-AATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT
genomic: ATCCTAGCTGTGTTGTTCGCCAATTCCGTTGGGAATGTTTTAATCGAAAGgttcgtactt ... tatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtggcttgtctagtctttattaccaaatcatcagaagcatttatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGTTAAGTTGGGAGCAGATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTC
                                           tttatctt  CT-rich tract
                 tctttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggatcaccaagtagagctgaaattaagggtgtctgatcaccaatacatgtggcttgtctagtctttattaccaaatcatcagaagcatttatcttgcagGTTCAATGGAGTACCAGCTGAGGAACGGCTCCACTGGCGATCTTTCTTGGTTAAGTTGGGAGCAGATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - -caccaag
- - - - - - - - -ctgaaat
- - - - - - - - - - - - - - - - - - - caccaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaagca