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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G47770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
gta-taccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
||| |         |||  ||      |   || | | ||||  |     | |    |        ||   ||| || | |||| ||  |  |   ||  ||||||||| ||||||||||| ||||||||||||||||||||||| ||||||   || || ||||| || ||||||||||| || || ||||||
gtaatgttttctccaaatgctatcttgtaggatgtttgttagccaagtgaagttatatg-------ctaagtgtggc-accactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG

upper sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
gtataccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
            ||| |  ||| |||    | || |   | |||| | | |           ||   | |  | |||  | || | | |     || ||| || |||| |||||||| || || |||||||||||||| |||||| | |||  |||||| |||||||| ||||| |||||  | || ||||||
-----------gtaatgctttaacctc---aactttccgaataatgggtgcaaa--------tcaactaaaattgct-cctctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG

upper sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
gtataccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
   ||| | | |        | | ||||||| |  | ||  |  || | |   |    | |||     ||||    | | | |||   ||||  ||||||| |||||| ||||||||||| ||||||||||||||||||||||| |||||    || || ||||| |||||||||||||| ||||| || |||
--gtactacttacttctgtgt-tgctttcaagcattttttatgtta-acagaatgaattttctgctaatatgaaattttaaatcac--tatttcttatctt-gcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG

upper sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
gtataccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
   ||| | |         || |  |||| |||  | ||| || || |||   | |  | |||     | ||    | | | |||   ||||  || ||||  ||||| ||||||||||| ||||||||||||||||||||||| |||||    || || ||||| || ||||||||||| ||||| || |||
--gtactagttccttctgtttgt--tttctatcatttttaatatta-atagattgcattttctgctaatttggaattttaattcac--tatttcttgtctt-acagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG

upper sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G168681_T01 (Zea mays), 3'ss of exon 3
gtataccaatgataaagacttatcctttcaatctctattagtaatag-atactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
                 | || |  |||    | | | |  |   || | |    ||  ||       | |    |      || |      || |  | ||| ||||| || ||||  || ||||||||||||||||| |||||| |||||  |||||| || || || |||||||||||||| || ||||||
---------------gtatttttttttttgtcccccactgttgccaggaaaaatgccagtcaaggaactgagagtggctcatctaagttcgctcgtcgtattt-cagCTTCAGGCTTTCTTTCTTGTGCTTGATGATATCATGGATGACTCTCACACTCGTCGCGGCCAGCCTTGCTGGTTCAGGGTGCCTCAG

upper sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
gtataccaatgataaagacttatcctttcaatctctattagtaa--taga--tactctcctctctctctctttatgtcgctatca--------ctcatca-----tattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
||||  |  |   ||    ||  | ||    | |  || | |||  |||   || ||   ||      |   | ||  |  ||          || || |     | || ||    ||||||||| || || ||||| ||||| |||||||| |||||||||||||||  ||| ||||||||||| || |||||||| ||||| ||  ||
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG

upper sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
gtataccaatgataaagacttatcctttcaatctct-attagtaatagatactctcctctctct-----ctctttatgtcgctatca------ctcatcat-----attcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
   ||   | | | ||  ||||| ||||   | | | | |  | |||     |||  ||  |        |   | ||  |  ||        || || ||      || ||    ||||||||| || || ||||| ||||| |||||||| |||||||||||||||  ||| ||||| || || || |||||||| ||||| ||  ||
--gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG

upper sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtataccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
                      |     |  | ||| || |  ||||   ||      |  |  | |        || || |   |  ||| |  | |    | || | |  ||     |||||||| ||||| |||||||||||||||||||||||||||||||||||    || || || |||||||||||||||||||| |||||  ||
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|124725924|gb|EH817326.1|EH817326
EST:     GTGCATTGAATGG                         CTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACT
genomic: GTGCATTGAATGGgtataccaat ... atctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
                                           ttatcttt  CT-rich tract
                                    atattcattatcttt  TA-rich tract