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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggctaccttacacttaaaagtcaaaaatttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G53900.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G132251_T01 (Zea mays), 3'ss of exon 4
gtacgttttcaatcttaaattttattttttggttagatgtagaaat--ttatgatcctgatggctaccttac---acttaaaagtcaaaaatt--tattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
   ||  |   | |   |||   |      |     | | || |||     | || |    | |   |||||   | |     |||     ||  | |||||||||||||| |||||||||||||| |||| ||||||||| |||
---cgcctgtcaccaagaatcaaacgccacgaaacaacgcagtaataacctttattcctgcgccgctcttacccaattcccctgtcggcttttgctgttgcagCTTCCTCCGGAATGGACCGACCAGTTCGCATCAGGCATCCAG

upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 4
gtacgttttcaatcttaaattttattttttg--gttagatgtagaaatttatgatcctgat-ggctacctta--cacttaaaagtcaaaaatttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
    || ||   | ||   ||||  |  | |   |||  |||||   |||    |  |||| |  |  || |  ||| |          |||| ||||||||||||||| |||||||| ||||| || || ||||||||||||
-ccagtgttgtgttttgtttttttctggtggttattatgtgtagctgttttgtttgatgattgattgactcaaccaccttttgtgatgcaattaattgcagCTTCCTCCTGAATGGACAGACCAGTTTGAGTCAGGCATTCAG

upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 3
gtacgttttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggctaccttac---acttaaaagtcaaaa----atttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
   |  | |    |||   |||| | |  ||||||  | |     | | |     |||||  |   | ||   || |     |    |    ||| ||||||||||||||| |||||||| ||||| || || ||||||||||||
--ccagtgttgtgctttgtttttttctggtggttat-tatgtgtgtctgtttgtttgatgattgattgactcaacctcctttttgtgatgccattaattgcagCTTCCTCCTGAATGGACAGACCAGTTTGAGTCAGGCATTCAG

upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 4
-------gtacgttttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggct-accttacacttaaaagtcaaaaatttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
          |    | |   |||||||||   | |||||||  |||||  |||||         || || | | | | |||     |     ||||||||||||||||||| |||||||  || || || || ||||||||||||
ccaagtttagcaaagttagcattaaatttt--ctattggttatgtgtagctatttagtgattgattgtctcaacctcctctttctgat--gttatttattgcagCTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG

upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 4
-------gtacgttttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggct-accttacacttaaaagtcaaaaatttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
       ||  |  |||||| |  |   || | | |||||||  |||||  || |          || || | | | | |||     |     ||||||||||||||||||| |||||||  || || || || ||||||||||||
tagcaaagtcagcattcaattt--agccttttctattggttatgtgtagctatatggtgattgattgtctcaacctcctctttctgat--gttatttattgcagCTTCCTCCTGAATGGATAGATCAGTTTGAGTCAGGCATTCAG

upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------------------------------------------gtacgttttcaatctt----aaattt-tattttttggttagatgtagaaatttatgatcc--tgatggct-accttacacttaaaagtcaa--aaatttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
                                                                                     ||   ||   ||  ||    ||||   |  |||||||    |||| |   | ||| ||    | |||  | |   |   ||||    |      |||| ||||||||||||||| ||||||||||| || || || ||||||||||||
gtaagtaggagaacctcaaacacaaacgttctcttttgattgggtatttgataaaactaattaccattgtgtgggcaaatagtgggtgatttgataaatttggagaaatgggttctttttggcatcatgtcgtggtctattatatgttaatgattgatgatgttcttagcttttggttgaattaattgcagCTTCCTCCTGAATGGACCGATCAGTTTGAGTCAGGCATTCAG

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|124881202|gb|EH960104.1|EH960104
EST:     TTACTGGCAAAGTTCTTTTGATGCT                         CTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
genomic: TTACTGGCAAAGTTCTTTTGATGCTgtacgttttc ... tttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatttatgatcctgatggctaccttacacttaaaagtcaaaaatttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
                      accttac  putative branch site (score: 3)
                             acttaaaagtcaaaaa  TA-rich tract