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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcattgcaattagaatcttttaactcccggttatgatttggtactaaaccactctctcatgctatttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA

Basic information

species Arabidopsis thaliana
transcript AT1G53310.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
------gtatcattgcaattagaatcttttaactcccggttatgatttggtactaaaccactctctcatg----ctatttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA
           |    |   | ||  |  | |||      || | ||||||  |   |  ||   | | |    ||  || || |||||||||| |||||||||||||||||| | ||||| ||| | |||||||||  | | || |||||||| || |||||||| ||  |  ||||||| || |
gtacataggctaagatacaaaaaacttgcttactatgctatacgttttggt--tgtccttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA

upper sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 7
gtatc---attgcaattagaatcttttaactcccggttatgatttggtactaaaccactctctcatgc-tatttgtgt--------agTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA
||||    ||| | |  | ||     ||| | ||   ||| |  |  |  | ||| | | | | |  | ||||| | |        || | ||||| ||  | ||||| || ||| | || |||||  | |||||||| ||| | || || |||||||||||||||||||||||| | ||||| || |
gtatagaaattcccagcaaaaatcaataatttccatgtataacata-tgttcaacgattttttaacacatatttatcttctgtttcagCTATTGGAGCCCTTGGAGCTATGCTACAGGTCGCTGTGCGCCTGTGGTGACCGTGCCATCGCTGATGGAAGCCTTCTTGATTTCTTGCGCCAAGTTTCCA

upper sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
---------gtatcattgcaatta-gaatcttt-taac---tcccggttatgatttggtac-taaaccactctctca---------tgctatttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA
           || |     || | | |||||| ||||   |   || |||  | || |   |  |      ||||          |  |  |  || |||||||||| |||||||||||||||||| ||||||||||| | |||||||||||  |  | || ||||||||||||||||| ||||| |||||||| ||||
caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA

upper sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------gtatcattgcaattagaatct-tttaactcccggttatgatttggtactaaaccactctctcatgctatttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA
                         ||      |  |||  | | ||| | | | | || |  |||  |  |  |    | |    |    ||| |||||||| | || |||||||| ||||| ||  |||| || ||| | |||||||| || || || || |||||||||||||||||||| ||| ||||||| || |
gatgttttcattatcagattttgcaatttgcatagatagtgtatattttagtactgatttttgtttttttttttaaatttttaatttttattttctgtagTTCCTAGAGCCTCTTGAACTCTGCTATAGATCACTCTGTGCTTGTGGTGACCGGCCTATTGCTGATGGAAGCCTTCTTGATTTTTTGCGGCAAGTTTCTA

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|164215701|gb|ES013972.1|ES013972
EST:     TGGACACTCTGATGTCCCTGTAGAGGCTACTTTCATTAACTTGGAACAG                         TTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGA
genomic: TGGACACTCTGATGTCCCTGTAGAGGCTACTTTCATTAACTTGGAACAGgtatcattgc ... atttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGA
EST: gi|164210418|gb|ES013202.1|ES013202
EST:     ATGGACACTCTGATGTCCCTGTAGAGGCTACTTTCATTAACTTGGAACAG                         TTCTTGGAACCTCTTGAGCT
genomic: ATGGACACTCTGATGTCCCTGTAGAGGCTACTTTCATTAACTTGGAACAGgtatcattgc ... atttgtgtagTTCTTGGAACCTCTTGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactcccggttatgatttggtactaaaccactctctcatgctatttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA
                       tactaaa  putative branch site (score: 1)
            ttatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcattgcaattagaatcttttaactcccggttatgatttggtactaaaccactctctcatgctatttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG