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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA

Basic information

species Arabidopsis thaliana
transcript AT4G26570.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 4
------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaaga--taacttgacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
              |  |   | | |  ||      ||      || | | |||  |    | ||   | |      |||  |        |  | ||||||||| ||||||||||||||||| || ||||||||  | || ||||| || ||||| ||||| ||||| || |||||||||| ||||||  | || || |
aattctttgtagaaaaatagctgtatgatagatgtcagtgcagattttgcctttatctccgtgctgcctcatgttcttaatattctccctgctcttacagGTATTTGATTTGTTTGACACAAAACACAATGGAATTTTAGGATTTGATGAATTTGCTCGTGCACTCTCAGTATTTCATCCAAGTGCTCCACTTGATGAGA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
--------------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaa-gatcctttttgaaagataacttgacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
                    | |  || |   |   | |||       || ||||   || |   |   ||| | |    || ||  ||||       |  |  |||||||| |||||||||||||||||||| ||||||||  | || ||||| || ||||| ||||||||||| || |||||||| ||||||||| | || || |
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgct-tttggttactgatataaaagtaatcatgtccctaatattccttg------tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 4
------------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
                    |  || |   |  || |||       || ||||   || |   |  ||    | |     |||  ||     |  | ||   ||||||| ||||| |||||||||||||| | ||||||  |||| ||||| || ||||| ||||||||||| || |||||||| ||||||||| | || || |
tagaaaaattagctgcacaaaaattgtggatccttgatcttgct-tttggttactgatataaaagtatatcatgtccctaatattttct---tgtccattgtagGTATTTGATTTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 5
gtatgttcttcttttttaatcaaaagactttgtt-----atccatttgcca---agatcctttttgaaagataacttga------cagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA-
 | | | | | || ||| | ||  | | ||||||     ||  |||  | |   |  |  |  ||| ||  |||  |||      |  || |  |   ||||||| ||||| |||||||||||||| ||||| ||||| || ||||| |||||||| ||||||||||| || |||||||||||||| || || || || | 
-tgtttacgtattatttcaacattatattttgttcaaaaattgattcacaattcaacttgtgattggaatctaatatgaacttctctctaactctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTTCATCCAAATGCCCCTATTGATGATAA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
-----gtatgttcttcttttttaatcaaaagactttgtt----atccatttgccaagatcctttttgaaagataacttgacagtaccaatcac------agGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
      | | | | | ||||| ||| |  | | ||||||    |     ||  ||  |  | || ||   | || ||     | ||   || |      ||||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||||| ||||||||||| || || ||||| ||||| ||||| || || |
tatatctgtttacgtatttttcaat-attatattttgttcaaaaattgattcacattactccttgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
-----------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
                   | |||  |    |    |  | | |    |||| || |       |    | |       || | ||    ||||       |||| || || |||||||| |||||||| ||||| ||||| |  ||||| |||||||| ||||||||||||||||||||||| ||||| || || || || |
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgatttt---gtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G01870.2 (Glycine max), 3'ss of exon 4
gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaag----------------ataactt----gacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
        ||  |||  ||||||     |    ||| |||||   | ||||| ||||  ||                 || | ||         |||   |   |||| || || ||||||||||||||||||| ||||||||| |  ||  | |||||||| | ||||||||||||||||||||| |  ||  | || || || |
------agttactttgaaatcaatcacatgccatatacatttaatatgatcccttttagaaatgtatttgtgctattcatgatttttatattgttacattttgtagGTGTTTGACTTGTTTGACACAAAGCATAGTGGAATACTTGATTTCAAAGAGTTTGCACTTGCTCTCTCTGTCTTTCATCCCAGCGCATCAATTGATGATA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 4
gtatgttcttcttttttaa---tcaaaagactttgttatccatttgccaagatcct------ttttgaaagataacttgaca-----gtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
 |||| |||  ||  ||||   | |   |  |    ||| ||| ||    || |||      ||||    |     || |       ||||   |   |||| || || |||||||| |||||||| || || ||||| |  ||||| |||||||| || |||||||||||||||||||| ||||| || || || || |
ttatgatctgattacttaagagttagttgtatgccatatacatatgatgtgaaccttagaatttttatttgtcctgttcatgattttgtactgtttgtagGTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAGTTTGCACGAGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 3
gtatgttcttctttt--ttaatcaaaagactttgttatccatttgccaa--gatcctttttgaaagat------aacttga----cagtaccaatc--acagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
  |||||| |   ||  ||       || |||  ||     ||| | ||  ||  |    | ||  ||      || ||      |  | | ||||    ||||||| || ||||||||||||||||| ||||||||||| |  ||||| |||||||||||||| ||||||||||||||||| ||||| ||||| |||||||
--atgttccttcattagttggcttgtagtcttctttcagttttttcaaaatgagtccaaataaattattcctacaatttatgcctctattcaaatcttgtagGTATTTGACTTGTTTGACACAAAGCACAATGGAATACTAGATTTTGAAGAGTTTGCGCGTGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACA

upper sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaagatcctttttgaaagataacttgacagtaccaatca----cagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
              ||   |  |  ||| ||   |    ||||  |    ||    ||||  ||  ||      |   |    | | | |||||     ||||||| || |||||||||||||||||||| |||||||| || |||||||||||||| |||||||| ||||| ||||| || || || || || || ||||
aactcttgcatcattgaattggtagtttcattggatatttttgg-aagagttccaaaagacgctcatttgccattgtatatgtaatgctaatcaattgtagGTATTTGACTTGTTTGACACAAAGCATAACGGAATACTTGGCTTTGAGGAGTTTGCTCGTGCTCTATCTGTTTTTCACCCCAACGCACCTATCGACGACA

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|124818760|gb|EH903626.1|EH903626
EST:     GAGCTTGTTTGCAGACCGG                         GTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAG
genomic: GAGCTTGTTTGCAGACCGGgtatgttctt ... ccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAG
EST: gi|124880486|gb|EH959388.1|EH959388
EST:     TTGTTTGCAGACCAG                         GTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAG
genomic: TTGTTTGCAGACCGGgtatgttctt ... ccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAG
EST: gi|125097118|gb|EL153683.1|EL153683
EST:     GAGCTTGTTTGCAGACCGG                         GTATTCGATTTGTTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGA
genomic: GAGCTTGTTTGCAGACCGGgtatgttctt ... ccaatcacagGTATTCGATTTG-TTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatccatttgccaagatcctttttgaaagataacttgacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
                     tttttgaaagataa  TA-rich tract