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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtgtatagtgtttgtgtagtttgtttactcatgtggattttttcgaagtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT

Basic information

species Arabidopsis thaliana
transcript AT4G32660.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
cgtgtatagtgtttgtgtagtttgtttactcatgtggatttttt--cgaagtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
 |  ||||       ||| |||  ||| |||||   | |||         |     ||  |||   ||  || || | |||| |     |||||  |  ||||| || ||||||||||||||||| |||| ||| |||||||||||||||| ||||    | || ||| |||  ||||| ||||| |||||| | || || |
tgcttataaaacagttgtcgttc-tttgctcataaaggtttgccgatatggaaacaaatcaaagataatttttct-tcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
cgtgtatagtgt--ttgtgtagtttgtttactcatgtggattttttcgaa--gtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
  |  | |||    |  | | |||  || |||||||  | ||   ||  |  ||    || | ||   |  |||  | | |||| |     ||| |  |  ||||| || ||||||||||||||||| |||| ||| |||||||||||||||| ||||    | || ||| |||  ||||| ||||| |||||| | || || |
--ttgacagtaaaatcattttgttc-ttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttat-tcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 4
cgtgtatagtgtttgtgtagtttgtttactcatgtggattttttcgaa--gtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
| ||||   |  |  | | |||  ||  ||| ||  | ||   ||  |  ||    || ||||   |  |||  | | |||| |    |||| |  |  ||||| || ||||||||||||||||| |||| ||| |||||||||||||||| ||||    | || ||| |||  ||||| ||||| |||||| | || || |
cctgtagtatagtctttttgttc-ttcgctcgtgaaggttccctcatatggtcacaaattaaaaatattctttat-tcaatggatatcaatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 4
cgtgtatagtgtttgtgtagtttgtttactcatgtggatttttt---cgaagtttggaactaaac-ggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
    |||||||  |   |  | | | |   ||||||| |||| |    | | ||   |||||| | | ||| ||||| | |||| | | |||||||| || ||||| || ||||||||||| ||||| || ||||| |||||||||||||||||||||| | |||| ||| |||  ||||||||||| |||||| | |||||||
----tatagtggattgtttttatatatgtccatgtgggttttattcatggatttgataactaagcagaaacattcctttcaatgcattttaatggtgttatcagGTCTTTGAGAAGCTTGGACCAAGCTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTCCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT

upper sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 5
cgtgtatagtgtttgtgtagtttgtttactcatgtggattttttc---gaagtttggaactaaac---ggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
    | |  |  || || | ||  |||   | |||||| ||  |     |   | | |||| |||   | || |||||| |||||| ||| |||||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||||||||||||||||| | |||||||| |||  ||||||||||| |||||| | |||||||
----tgtgatagtt-tg-aattaatttctccctgtggacttcattcataagactggaaacttaacattgaaatcttcctttgaatgcactttaatggtgttaccagGTGTTTGAGAAGCTTGGACCAAGTTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTTCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT

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|163990545|gb|ES114651.1|ES114651
EST:     CTGTGTACAGATGAAGAACTGGTTTGATTACCGAAATCATATTTGCATT                         GTGTTCGAGAAGCTTGGGCCAAGTTTGTT
genomic: CTGTGTACAGATGAAGAACTGGTTTGATTACCGAAATCATATTTGCATTgtaagtatcc ... gtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTT
EST: gi|116384701|gb|EG427293.1|EG427293
EST:     CTGTGTACAGATGAAGAACTGGTTTGATTACCGAAATCATATTTGCATT                         GTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAA
genomic: CTGTGTACAGATGAAGAACTGGTTTGATTACCGAAATCATATTTGCATTgtaagtatcc ... gtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT
         aactaaa  TA-rich tract