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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcttttgtggtagactctgattttgatactctacaaaggtcatttaatctcttagctgaccaggttttgttttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG

Basic information

species Arabidopsis thaliana
transcript AT2G18510.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 3
gtaagtatcttttgtggtagactctgattttgatactctacaaaggtcatttaatctcttagc-tgaccaggttttgttttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
|| |    ||    |  ||   |||   ||  || |||| |||   |||| | |   || ||  |       |  |   ||  || | ||||||| |||||||||||| | |||||||| |||||||||||||| |||||||   |||||||||||
gtgaaggcctaa-atcctaatttcttcattatatgctcttcaat--tcatctgaatactgagtatatttttatgcttgctttgttaacagGATGTTGATGAGAAGCTCCTCTATGATACCTTCAGTGCATTTGGAGTGATTGTAACTAATCCTAAG

upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 5
--gtaag--tatcttttgtggtagactctgattttgatactctacaaaggtcatttaatctcttagctgaccaggtttt---gttt---tcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
  | | |  ||  |  |    |  | | | |  |    | |  |      ||| |  ||||     ||||  |  ||||   ||||   |  || | ||||||| ||||| |||||| | |||||||| |||||||||||||| |||||||   |||||||||||
gtgaaggcctaaatcctactctttattatcagctcttcaattcatttgaatcaatccatctgaatactgagtatattttcatgtttgcattgttaacagGATGTTGATGAAAAGCTCCTTTATGATACCTTCAGTGCATTTGGAGTGATTGTGACTAATCCTAAG

upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 5
gtaagtatctt--ttgtggtagactctgatt--ttgatactctacaaaggtcatttaatctcttagctgaccaggttttgttttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
||||||  |    || ||| ||  |   |     | || |  |       | | || |   ||||         |||     |  | ||  ||||||| |||||||||||||||||||| ||||||||||||||||| || |||| | ||||||| |||
gtaagtcaccaaattatggaagtgttaaacagactcatgcagttatgcattgaattcaagacttatacatgagtgttcctaatgttgttgcagGATGTAGATGAGAAGCTCTTGTATGACACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG

upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 5
gtaagtatcttttgtggtagactctgattttgatactctacaaaggt-catttaatctcttagctgacca--ggttttgtt--ttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
||||||| |     |     | | | | |  ||  |  | ||    | |||| |||     |  | | ||   || ||  |  |  | ||  ||||||| || ||||||||||||||||||||||||||||||||||| || |||| | ||||||| |||
gtaagtaaccaaattatgcaagtgttaatcagactca-tgcagttatgcattgaattcaagacttaaacatgagtgttcctaatgttgttgcagGATGTAGACGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGAGTTATTGTTACTAATCCAAAG

upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------------------gtaagtatcttt-----tgtggtagactctgattttgatactctacaaaggtcatttaatctcttagctgaccaggttttgttttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
                                                      | |  | ||||     ||||   |||||       | |  | ||  |      || ||| |   || |||||     | | | |  |||  |||||||||||||||| ||  ||||||||||||||||||||||||| || ||||   | ||||| |||
gtaagtagttcaattccttatttttatttatttttattgggaagttgtattgtatcaaaacctttgtgggtgtgaaggactcatggacagttgttgtatcactagt-ttcaattttaaagttgacc----ctggatgttctttgcagGATGTGGATGAGAAACTTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAG

upper sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S70_254V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------gtaagtatcttttgtggtagactctgattttgatactctacaaaggtcatttaa--tctcttagctga--cca-ggttttgttttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
                                                                               |  | | | | |||    |  | |  |  ||| | |  |     ||  || ||  ||||     |||  ||| | |||   ||   | |  |||||||||||||||| || ||||| |||||||||||||| ||||| ||||| |   | || ||||||
gtaagtcacactaatggttactttgttctaggaatgaaacagtgttatttctggttttaggttagacctgtcttacttatctgcagcctatgttcgtggatgttctaatgaaagtgaagcctagtgcttcaaaatctcgagaatgagcccatgatttcccttggctgtgcagGATGTGGATGAGAAACTATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAG

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|125164522|gb|EL191219.1|EL191219
EST:     CTAACCTTTTCATTGGAAACCTTGACCCT                         GATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATT
genomic: CTAACCTTTTCATTGGAAACCTTGACCCTgtaagtatct ... tcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctacaaaggtcatttaatctcttagctgaccaggttttgttttcttttatagGATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAG
                          agctgac  putative branch site (score: 3)
                                     ttttgttttcttttat  putative PPT
                                     ttttgttttcttttat  TA-rich tract