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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcctcttttacttctcttcttatctttcatctcaatgctcattttgtatttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG

Basic information

species Arabidopsis thaliana
transcript AT4G17190.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
--------------------------gtaattcctctttta--cttctcttcttatct-ttcatctcaatgctcattttgtatttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
                          |||     | | |||  |   |    |||| |  | |        |   |  ||  | ||| |   ||||||||||||||||||||| |||||||||||||| || ||||||||||||   ||||| |||||||||||||| ||||||||   |||  ||             
gtaatgttttctccaaatgctatcttgtaggatgtttgttagccaagtgaagttatatgctaagtgtggcaccactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG-------------

upper sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
gtaattcctcttttacttctcttcttatctt---------tcatctcaa--tgctcattttgtatttgc--ttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
||||| | |      |  || | |  ||  |         ||| || ||  ||||| | |    ||| |  |||  | || ||||||||||||| || || ||||||||||| ||||||||  | |||  ||| || ||||| ||||||||||||||| |   |||  ||             
gtaatgctttaacctcaactttccgaataatgggtgcaaatcaactaaaattgctcctctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG-------------

upper sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
---gtaattcctcttttacttctcttcttatctttcatctcaatg---ctcattttgtatttgcttgca----------------------tttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
    || |||||  | |   | |  | | || ||| || | |||      |||||| |  |   ||| |                       || ||||||||||||||||| |||||||||||||| || |||||||||||    ||||| |||||||||||||| |||||||||  |||| ||             
gtactagttccttctgtttgttttctatcatttttaatattaatagattgcattttctgctaatttggaattttaattcactatttcttgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG-------------

upper sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
----------------------------gtaattcctcttttacttctctt--cttatctttcatctcaatgctcattttgtatttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
                            | | ||  | | |||      |    ||     | || | ||   | |  |     || |||    |||||||||||||||||||| |||||||||||||| || |||||||||||    ||||| |||||||| ||||| |||||||||  |||| ||             
gtactacttacttctgtgttgctttcaagcattttttatgttaacagaatgaattttctgctaatatgaaattttaaatcactatttcttat-cttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG-------------

upper sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G168681_T01 (Zea mays), 3'ss of exon 3
gtaattcctcttttacttctc-ttcttatc--------tttcatctcaa----------tgctcattttgtatttgcttg-cat-ttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
||| ||  | ||||    | |  | ||  |        |  ||    |           ||     | |   || ||| | | | || |||||||| ||||  || |||||||||||||| ||||||||  |||||  ||| || || ||||||||||| ||||| ||   |||  ||             
gtatttttttttttgtcccccactgttgccaggaaaaatgccagtcaaggaactgagagtggctcatctaagttcgctcgtcgtatttcagCTTCAGGCTTTCTTTCTTGTGCTTGATGATATCATGGATGACTCTCACACTCGTCGCGGCCAGCCTTGCTGGTTCAGGGTGCCTCAG-------------

upper sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
------------------------------------------gtaattcctctt-ttacttctcttcttatctttcatctcaatgct-cattttgta-------tttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
                                           || |   |||  |   |||   | ||  || | ||  || ||    || || |        |||| | |  |||||||||||| || ||||| ||||| ||||||||||| ||||| ||||||  ||||||||| |||||||| || |||||||||  ||| |||             
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG-------------

upper sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------gtaatt-cctcttttacttctcttcttatctttcatctcaatgctcattttgtat-ttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
                                                    ||||    ||   |  ||    |  |  | ||       ||  |    |||| | ||| | |  |||||||||||| || ||||| ||||| ||||||||||| ||||| ||||||  |||||||||||| ||||| || |||||||||  ||| |||             
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG-------------

upper sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------gtaattcctcttttacttctcttcttatctttcatctcaatgctcattttgtatttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
                                                          ||     |   | |      ||| | || |||  ||||       || | ||   |  || |||||||||||||| |||||||||||||||||||| || ||||| |||||    ||||| || || || ||||| ||||| ||    || |||             
gtaggcaacagaatacctcccctgtattttgttaaggctgaagctttttctcaggtccataatcataccagtgtatcgcttttgttgcatgacaatttatgccttcttttctatgccacttgcagCTTCAAGCATATTTCCTTGTGCTTGATGATATTATGGATAACTCGCATACACGTCGAGGTCAACCTTGCTGGTTCAGGGTTCCCAAG-------------

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|164182207|gb|ES088130.1|ES088130
EST:     AGACTTTCCTCTCATGTGCTCTTGGTTGGTGCATTGAATGG                         CTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTC
genomic: AGACTTTCCTCTCATGTGCTCTTGGTTGGTGCATTGAATGGgtaattcctc ... gcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcttcttatctttcatctcaatgctcattttgtatttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
                              attttgtattt  TA-rich tract