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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagtgcttttctttttgcctttccttgttttcattcttctttgttaagcgaacagcttcttattcgaaaattgtattccttcagGTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTATGATAAACAACTAGACAGCGGGAGGGGAACGCTACTACATTTGTGTGAT

Basic information

species Arabidopsis thaliana
transcript AT3G19340.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g70390.1 (Oryza sativa), 3'ss of exon 11
------------gttaagtgcttttctttttgccttt---ccttgttttcattcttctttgttaagcgaacagcttcttattcgaaaattgtattcc-ttcagGTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTATGATAAACAACTAGACAGCGGGAGGGGAACGCTACTACATTTGTGTGAT
             || ||   |||  | |||    |    | || ||| |  | ||  ||||  |  | |||  || |  |    ||  |   ||   |||||||| || ||||||||||| || ||||| ||| | |||||||| ||||||||||| ||||| ||||| || ||||  || || || || ||| | ||||||
cttccctgattccttcagcattttcttatttatgatgatactttatttgctgtattggttgt--attggacaaatt-tggtaaataagctacctttgattcagGTTTCAACAGAACATGGCAACATATCAAAACCTAATAACTCAATCAATGTATGACAAACAGCTAGATAGTGGGAAAGGCACACTTCTCCATCTCTGTGAT

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G161168_T01 (Zea mays), 3'ss of exon 11
---------gtta-agtgcttttctttttgcctttcc-ttgttttcattcttctttgttaa-gcgaacagcttcttattcgaaaattgtattcctt-cagGTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTATGATAAACAACTAGACAGCGGGAGGGGAACGCTACTACATTTGTGTGAT
          ||| | || | ||| || |    ||   | |       | |     || |  | |    ||    | ||  | | || | ||   | |||||| || ||||| ||||| || || || ||||| || ||||| ||||||||||| ||||||||||| || ||||  || || || || ||  | ||||||
ctttccttcattagaatgatattccttatatggttgtgtcgggcattatgtaaacagtcatcgtgttgggcagtctgttgaatagttatgttttatgcagGTTTCAACAGAATATGGCAACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGAT

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G05180.1 (Glycine max), 3'ss of exon 11
----gttaagtgcttttctttttgcctttccttgttttcattcttctttgttaagcgaacagcttc--------ttattcgaaaattgtattcctt-cagGTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTATGATAAACAACTAGACAGCGGGAGGGGAACGCTACTACATTTGTGTGAT
     | |    |   || |  |   ||    ||| |  |      |   ||     || |  ||         ||      || || | |||| |  ||||||||||| |||||||||  ||| || || ||||| || |||||||||||||| |||||||| ||||| || | ||| ||||| || ||||||||||||
cattatcattgccgcatcctactagtttgtgatgtatagaagtaaatgcatttgaaaaagatttttaaccctagttgcctctaatttcttttccctatagGTTCCAGCAAAACATGGCTCAGTACCAAAATTTGATTACGCAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACGCTTCTTCATTTGTGTGAT

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 11
-----------gttaagtgcttttctttttgcctttccttgttttcattcttctttgttaagcgaacagcttcttattcgaaaattgtattccttc--agGTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTATGATAAACAACTAGACAGCGGGAGGGGAACGCTACTACATTTGTGTGAT
           |     | ||  |  |||    | |       |  || | | |     |       | | |  |   |   ||||   || |  |  |||||||| || |||||||||  ||| || || ||||| || |||||||||||||| |||||||| ||||| || | ||| || || || ||||||||||||
gcattattattgccgcattctactagtttgagatgtatagaagtaaatgcatttgaaaaagatatttaacctagttgccactaatttcttttccccatagGTTCCAACAAAACATGGCTCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGAT

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|164227432|gb|ES070166.1|ES070166
EST:     GTTATTGTGCGAAAACATACTTCAC                         GTTCCAGCAGAACATGGTCTACGTATCAGAACTTGATAACTCAGTCAATGT
genomic: GTTATTGTGCGAAAACATACTTCACgttaagtgct ... attccttcagGTTCCAGCAGAACATGG-CTACGTATCAGAACTTGATAACTCAGTCAATGT
EST: gi|86055111|gb|DR350868.1|DR350868
EST:     ATTGCCATTCTCTCCACAGTGCTTGGTTATTGTGCGAAAACATACTTCAC                         GTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTA
genomic: ATTGCCATTCTCTCCACAGTGCTTGGTTATTGTGCGAAAACATACTTCACgttaagtgct ... attccttcagGTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattcttctttgttaagcgaacagcttcttattcgaaaattgtattccttcagGTTCCAGCAGAACATGGCTACGTATCAGAACTTGATAACTCAGTCAATGTATGATAAACAACTAGACAGCGGGAGGGGAACGCTACTACATTTGTGTGAT
                                            tattccttc  CT-rich tract
                                     aaaattgtatt  TA-rich tract