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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccctttcattgtttcttgaatatatcctaccaggtaattactctcatattcatacttagttcaatgtatgaatgttgtctggttttcagGTCGTGTCTGTGTTCCTATTGACCCGAATAACTGTGATGAGTTTGATCCATTGGCAGTTCCAACTCTTTCACAG

Basic information

species Arabidopsis thaliana
transcript AT5G41880.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G41880.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os05g29010.2 (Oryza sativa), 3'ss of exon 12
---------gtccctttcattgtttcttgaatatatcctaccaggtaattactctcatattcatacttagttcaatgtatgaatgttgtctggttttc-agGTCGTGTCTGTGTTCCTATTGACCCGAATAACTGTGATGAGTTTGATCCATTGGCAGTTCCAACTCTTTCACAG
          | | ||   ||  | |||  |  ||| |    |  ||  | ||  |  ||   | || ||||| |   ||   | |    |  ||  | ||| ||||| |||||||| || || || |||||||||||||| ||||||||   | ||||||||||||| ||||||
cacatttatatgcattcatttcatgcttacacttatac-gtaaaatatgttctgcctaatgagttctaagttctaacaattgttttgaaatctttccctagGCCGTGTTTGTGTTCCAATCGATCCAAATAACTGTGATGATTTTGATCCTACGACAGTTCCAACTCTGTCACAG

upper sequence: AT5G41880.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G439297_T01 (Zea mays), 3'ss of exon 1
----gtccctttcattgtttcttgaatatatcctaccag--gtaattactctcatattcatacttagttc---aatgtatgaatgttgtctggttttcagGTCGTGTCTGTGTTCCTATTGACCCGAATAACTGTGATGAGTTTGATCCATTGGCAGTTCCAACTCTTTCACAG
     ||| |  |||||||  || | | ||| ||| |||  | |   |   |  |  ||| ||   ||||   | ||     |  |        || |||| ||||| |||||||| |||||||| | |||||||||||| ||||||||   ||| ||||| ||||| ||||||
taaaatccttgacattgttgatttagtttattctaacagctgcaggaataatgtttgtcacacaatgttccctattgctcacaactgactcttcttccagGCCGTGTTTGTGTTCCGATTGACCCCAGTAACTGTGATGATTTTGATCCTGCGGCTGTTCCGACTCTATCACAG
















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|164173880|gb|ES059873.1|ES059873
EST:     ACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAG                         GTCGTGTCTGTGTTCCTATTGACCCGAATAACTGT
genomic: ACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAGgtccctttca ... tggttttcagGTCGTGTCTGTGTTCCTATTGACCCGAATAACTGT
EST: gi|164017049|gb|ES141105.1|ES141105
EST:     ACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAG                         GTCGTGTCTGTGTTCCTATTGACCCGAATAACTGTGATGAGTTTGATCCAT
genomic: ACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAGgtccctttca ... tggttttcagGTCGTGTCTGTGTTCCTATTGACCCGAATAACTGTGATGAGTTTGATCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattactctcatattcatacttagttcaatgtatgaatgttgtctggttttcagGTCGTGTCTGTGTTCCTATTGACCCGAATAACTGTGATGAGTTTGATCCATTGGCAGTTCCAACTCTTTCACAG
                                                ttttc  CT-rich tract
           atattcata  TA-rich tract