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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattttatgcttttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC

Basic information

species Arabidopsis thaliana
transcript AT1G08200.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 2
gtatgtattttatgcttttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacggattttagttgtgacattg--agtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
                                  || |    |  | || |    |  ||   | || || |    | |      |||| |    ||||    ||| | |  ||  || |    |||| || |||||||| ||||||||||||||||| || ||||| ||||| || || || || || || || || || ||||| || || |  || || ||||
---------------------------------gtaatccctcc-tcttctccactccagatttcttcttcttcttttctaccactagt-gcagaattgttgatggacgtgtgtgatg-tgcacagGTCAAGTACTGCTCTGAGAACAACAAGCGTCTCATCCACTTCTCCACGTGCGAGGTCTACGGCAAGACCATCGGCAGCTTCCTCCCCACCGACCACCCTC

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 2
gtatgtattttatgcttttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
            ||| | |    |||  ||   ||  |    |  |||| |  ||||          | | |||| |  | | || |        ||||||     |||||  || |  |  |||| || ||||| |||||||||||||||||||| ||||| || || || |||||||| ||||| ||||| || |||||||| || || || |||  |||||
-----------gtgcgtcttacttttactttactttctctcccttttttctttgttt----------tctgtgtgtttggaaattcaa-------attgagg----attggaatttgggttcagGTGAAGTACTGTTCAGAGAACAACAAGCGTCTCATTCATTTCTCTACGTGTGAAGTCTATGGGAAAACGATTGGAAGCTTCCTCCCCAAAGATAGTCCTC

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 2
gtatgtattttatgcttttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaat--atttttatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
                                  ||    | ||  | |  || ||  |    |  |    |   |  |  || ||| |||| |     || |  ||| ||  || || | ||||||| |||||||| || |||||||||||||| || || || || |||||||| |||||||| || ||||| || |||  |||||| || || |||  |||||
-----------------------------gtaactaactaaccacctgttcaaattgaaaatgtgaaacgctgaatcttgagggtttgagttcta----tgcgacgtcgtt--ttgtgctttgtagGTGAAATACTGTTCCGAGAACAACAAGCGCCTTATCCATTTCTCCACTTGCGAAGTGTACGGGAAAACGATTGGAGCCTTTCTCCCTAAAGATAGTCCTC

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 2
gtatgtattttatgcttttgcagtttgtttggtttagtggagcaattttgtaagtttgag-gaatatttttatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
                   | |  ||   |  || | |         || ||| |   |  |   ||| ||   |  |      |||   |  ||      || ||  || ||| |  | ||||||| |||||||| || |||||||||||||| || || || || || ||||| |||||||| ||||| || || |||  |||||| || || |||  |||||
-------------------gtaacttaactacttcactaactacccgttctaattgcaaatgtgaattgttgaatcttgaatgatttgagttcgattcgacgtcgt--ttcgttcttttttgtagGTGAAATACTGTTCCGAGAACAACAAGCGCCTTATCCATTTCTCTACTTGCGAAGTGTACGGAAAGACGATTGGAGCCTTTCTCCCTAAAGATAGTCCTC

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 2
gtatg-tattttatgctt-ttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
||||| | ||  |||||| ||  | || ||||   |    |||  ||| ||||   | | ||     ||||| |||    ||||  |  ||||   | |   |||    ||| | | | | | ||||| |||||||| || ||||||||||||||||| |||||||| || ||||||||||| ||||| ||||| || || ||||||||||| || |||   || |
gtatgctgttggatgcttgtttgaattcgttttcgtccaagga-taatattgt---tgttag-----tttttttgtttctcggaaatctgttgaagc-tgatgtgcgttttgatgtggctctttagGTGAAATACTGTTCGGAGAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCCC

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 2
gtatg-tattttatgcttttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacg--gattttagttgtgacattgagtggtcattggttttgg-tatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
||||| | ||  ||| || |     || |||    |        ||| |||| | ||       | ||| |  |  ||  |  ||   |  |     | |||| | |   || | | ||| | | ||||| |||||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| ||||| || || ||||||||||| || |||   ||||
gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgatttgcgttttgatgtggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ07025 (Selaginella moellendorffii), 3'ss of exon 2
gtatgt-attttatgcttttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
||| ||   | | |  | ||   ||||     || |  |       ||||   || ||||    | ||||||     ||    ||    ||  ||  || ||||   | ||            |||||| ||| ||||| || |||||||||||  |||| || ||||| || || ||||||||||||||||| || ||||||||| | ||  ||||   | |  
gtaagtcggtattttttcttagcgtttccagagtgtttttagttcttttttagagcttgatagttgtttttagagcttattttttgctttttggaacttaagtg---actgag---aacgaacagGTTAGATATTGCTCGGACAACAACAAGCGCTTGATCCATTTTTCTACGTGCGAAGTGTATGGAAAAACGATTGGAAGCTTTTTGCCCGAGGACAGTTCCT

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ18978 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtattttatgctt-ttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
||| ||   |  |  || ||   ||||     || |  |       ||||   || ||||    | ||||||     ||    ||    ||  ||  || ||||   | ||            |||||| ||| ||||| || |||||||||||  |||| || ||||| || || ||||||||||||||||| || ||||||||| | ||  ||||   | |  
gtaagtcggtagtttttcttagcgtttcgagagtgtttttagttcttttttagagcttgatagttgtttttagagcttattttttgctttttggaacttaagtg---actgag---aacgaacagGTTAGATATTGCTCGGACAACAACAAGCGCTTGATCCATTTTTCTACGTGCGAAGTGTATGGAAAAACGATTGGAAGCTTTTTGCCCGAGGACAGTTCCT

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|116456216|gb|EG498808.1|EG498808
EST:     CGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTG                         GTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
genomic: CGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTGgtatgtattt ... tggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
EST: gi|116471821|gb|EG514413.1|EG514413
EST:     CGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTG                         GTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
genomic: CGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTGgtatgtattt ... tggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
EST: gi|116456222|gb|EG498814.1|EG498814
EST:     CGCGTCCCCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTG                         GTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
genomic: CGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTGgtatgtattt ... tggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
EST: gi|124818139|gb|EH903005.1|EH903005
EST:     CATTGATGCTCTCCCAGTG                         GTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
genomic: CATTGATGCTCTCCCAGTGgtatgtattt ... tggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
EST: gi|116456221|gb|EG498813.1|EG498813
EST:     CGCGTCCCCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTG                         GTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
genomic: CGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTGgtatgtattt ... tggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
EST: gi|116456217|gb|EG498809.1|EG498809
EST:     CGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTG                         GTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT
genomic: CGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTGgtatgtattt ... tggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC
            attttagtt  TA-rich tract