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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaccagaatatttgtgatacttatattttatcatttgctcacagacgctattgttactgaacattttgcaaggtttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGCTTTAAAACG

Basic information

species Arabidopsis thaliana
transcript AT3G58170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G58170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g57510.1 (Oryza sativa), 3'ss of exon 4
gtatttaccagaatatttgtgatacttatattttatcatttgctcacagacgctattgttactgaacattttgcaaggtttct--atgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGCTTTAAAACG
||||||      |||||| |  |  | |  |||  |   |||   |    |  | | |      |  || |||  |  || |   ||  ||||||||||||||||||| |||||||| ||||| || |||||  |||||   || || | |
gtatttt-----atatttatccttttaacttttgcttccttgaaaaatatccttctagagttctattatgttgacatcttgcctgatccagGGCAATGATATGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG

upper sequence: AT3G58170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0051g00940.t01 (Vitis vinifera), 3'ss of exon 4
--gtatttaccagaatatttgtgatacttatattttatcatttgctcacagacgctattgttactgaacattttgcaaggtttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGCTTTAAAACG
   | | | |   | ||    ||| || |      | |  |||  |         ||||||  || | |||  | |  | |  | ||  |||| ||||| |||||| ||||||||||| | ||||||||||||||||| || || || | |
gtatgtgtgctgaagta---atgaaacctgctccatgtgttttaatt--------tattgtctctca-catgattct-gttcacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGGTTCAAGATG

upper sequence: AT3G58170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 4
gtatttaccagaatatttgtgatacttatattttatcatttgctcacagacgctattgttactgaacattttgcaaggtttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGCTTTAAAACG
|||| |        | || | | ||  || ||||    | | ||     |  | ||      || |         |  ||  |||  ||||||||||||||||| | ||||||||| | || |||||||| ||||| || ||||||| |
gtatgtgt-gctgcagttataaaacccat-tttttctgtgttcttgtttataccatctcatgtggat------tgattttgttattaagGGCAATGATATGGATGCTTCAAGGGGAATCCTATCAGGAACTATGGATCGATTTAAAATG

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|19877362|gb|AU238193.1|AU238193
EST:     GCGATATAAATGAAGAGGTCGATACTCATAACCGCATGCTTGACAGAATG                         GGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGC
genomic: GCGATATAAATGAAGAGGTCGATACTCATAACCGCATGCTTGACAGAATGgtatttacca ... ttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGC
EST: gi|124729328|gb|EH820730.1|EH820730
EST:     TAACCGCATGCTTGACAGAATG                         GGCAATGATATGGATTCATCAAGGGGAGTTTCTCTCAGGAACCATGGACCG
genomic: TAACCGCATGCTTGACAGAATGgtatttacca ... ttctatgtagGGCAATGATATGGATTCATCAAGGGGA-TTTCTCTCAGGAACCATGGACCG
EST: gi|116471650|gb|EG514242.1|EG514242
EST:     GCGATATAAATGAAGAGGTCGATACTCATAACCGCATGCTTGACAGAATG                         GGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGC
genomic: GCGATATAAATGAAGAGGTCGATACTCATAACCGCATGCTTGACAGAATGgtatttacca ... ttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGC
EST: gi|86060002|gb|DR355759.1|DR355759
EST:     GCGATATAAATGAAGAGGTCGATACTCATAACCGCATGCTTGACAGAATG                         GGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGC
genomic: GCGATATAAATGAAGAGGTCGATACTCATAACCGCATGCTTGACAGAATGgtatttacca ... ttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGC
EST: gi|86088029|gb|DR383788.1|DR383788
EST:     GCGATATAAATGAAGAGGTCGATACTCATAACCGCATGCTTGACAGAATG                         GGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGC
genomic: GCGATATAAATGAAGAGGTCGATACTCATAACCGCATGCTTGACAGAATGgtatttacca ... ttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatttgctcacagacgctattgttactgaacattttgcaaggtttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGCTTTAAAACG
      tgctcac  putative branch site (score: 2)
                                            tttctat  putative PPT
                   tattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaccagaatatttgtgatacttatattttatcatttgctcacagacgctattgttactgaacattttgcaaggtttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGCTTTAAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA