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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtgttcctgttctcactgttttgatttttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC

Basic information

species Arabidopsis thaliana
transcript AT5G25100.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
-----------gcaagttcttgtttga--ctaatcagtttatcaccagatagttttgtcttagtgagatactat-tgtgttcctgttctcactgttttgatttttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
           ||| ||| |  || ||  ||  |       |||   |||||||   | ||      ||  ||  | | || |  |  |  |  ||     |||| | || ||   | ||||| |||||  | |||||||| ||  | |||||  | ||||| |||||||  ||  |||| ||||||||||||||||||||||||||||| |||||||| |
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcat---tgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
gcaagttcttgtttgactaatcagtt-tatcaccagatagttttgtcttagtgagatactattgtgttcctgttctcactgttttgatttttgcgctgatg-tcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
           | |  |  || |  |   |   ||  |   ||    |   |   | | | ||| |||  | ||     | || ||||||    | |  || ||| ||||| |||||  | |||||||| ||| | |||||  | ||  | || ||||  ||  ||||||||||||||||||||||||| |||||||| |||||||| |
-------tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaat-ttgagtttgttttaatgtt-ttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G180575_T01 (Zea mays), 3'ss of exon 6
gcaagttcttgtttgactaatcagtt-tatcaccagatagttttgtcttagtgagatactattgtgttcctgttctcactgttttgatttttgcgctgatg-tcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
           | |  |  || |  |   |   ||  |   |     |   |   | | | ||| |||| | ||     | || ||||||    | |  || ||| ||||| |||||  | |||||||| ||| | |||||  | ||  | || ||||  ||  ||||||||||||||||||||||||| |||||||| |||||||| |
-------tgaatctatcacataaactgcgttgtcaagttactaaacatacatttcaaaat-ttgagttcgttttaatgtt-ttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
--gcaagttcttgtttgactaatcagtttatcaccagatagttttg-tcttagtgagatactattgtgttcctgttctcactgttttgat---ttttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
   ||||     | || |  | |  | ||||    |  | |||| | |  |||||   |  |    |||| || || |||   |||| ||     || | || ||   ||||||| |||||  | |||||||||||  | |||||  | || || ||||||| |||  |||| |||||||||||||||||||| |||||||| |||||||| |
gtacaagactgggattaagaatt--gcttattttaactttgtttagctgctagtgtactctttgaatgtttcttttgtcatgattttaatggaacttccactaat--tttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G039811_T01 (Zea mays), 3'ss of exon 6
gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtgttcctgtt-----ctcac-tgttttgatttttgcg---ctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
         |    |||| |    || |  ||    ||||||    ||  | || | || | |||| |   ||      | |  |||  ||||||    |   || |  | | ||||| |||||  | |||||||| ||  | |||||  | || || |||||||  ||  |||| ||||| |||||||||||||| |||||||| |||||||| |
--------gtacgagactga--gattaagaactgcttagtttaactttgtttagctgctgtagtgtactctttgaatgtttatatgtgatgatttcatggaacctcaattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G06460.1 (Glycine max), 3'ss of exon 6
gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtg--ttcctgttctcactgttttgatttttgcg-----ctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
               |||||     | |||      |  | ||||  |  | | ||   ||| ||   |    |||| | | | |    ||||||      ||| |  |||||||| ||||| ||||||||||| || ||||||||||||||| |  | ||||  ||  ||||||| |||||||| |||||||| |||||  | ||||| || |
--------------aactaacatcctcatcttttttttttgttgttatgataaaatgtgattatgggctgtatttcttattatctgctattttgcctttgtctggtaccttcagGAGAGTGACGTGAAGTGGGCTTCAAGATGGGATGCTTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCTATTGTTAACTCATTAATGATTGTTC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtgttcctgttctcactgttttgatttttgcgctga-tgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
      | ||||||     |||    |     ||  |   | |  ||        |   ||  |  || | ||||   ||   || ||||  |  ||  |   ||||||| ||||| ||||||||||| || ||||||||||| ||| |  ||||||| ||  | |||||||||||||| || ||||| |||||  | ||||| || |
------tattgtttcttccatccaagtggagtcatcttcctcttcctcctcttattctcatctttgtcatcttctt--tgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G11780.1 (Glycine max), 3'ss of exon 6
gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtgttcctgttctcactgttttgatttttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
 | |      ||     |  |||   |||   |   |   ||  ||||| |   ||  |  |||  || | ||    |||  || |  |||||     |   ||||||| ||| | ||||||||||| || ||||||||||| ||| |  ||||||| ||  | |||||||||||||| || ||||| |||||  | ||||| || |
tccaaggggagtcaccttcctcatcctattctcctcttccttc-tcttattctcatctt--tgtcatcttctttgacctgcctttacctttgcc----tacattcagGAGAGTAATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 6
gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtg--ttcctgttctcactgttt-tgatt--tttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
               | ||||  |||   | ||   |  | ||||  |  | | ||   ||||||   |    |||| | | | |   |||   ||  |||| |  |||||||| ||||| ||||||||||| || ||||||||||| ||| |  | ||||  ||  ||||||| |||||||| || ||||| |||||  | ||||| || |
----------agagaattaat--gttatccgcctttttttgttgttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC

upper sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 3'ss of exon 6
gcaagttcttgtttgactaatcagtttatcaccagatagttt--tgtcttagtgagatactattgtgttcctgttctcactgttttgatttttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
       |  |||| | ||||  ||  |   |||  | | ||  || |   || | |   |||| ||      |||| |  |||||  ||| |   ||      | ||||||||||| ||||||||||| |||||||||||| | |||||| | ||||| ||  | || || |||||||| || ||||| || ||| | ||||| || |
--ttaaccaagtttaa-taattggtgaaaagccaacttgcttgttgcccctgtta-aggttattatg-----attcttatggtttttttttctcatctctgccatacagGAAAGTGATGTGAAGTGGGCATCTAGATGGGATACCTATCTTCTCATGAGTGATGACCAGATCCACTGGTTCTCAATTGTTAATTCTTTGATGATTGTTC

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|116474271|gb|EG516863.1|EG516863
EST:     AAGTCGAAAATAAGAAAGAAATTATCTTCACATATGATGTTGACTTTCAG                         GAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGC
genomic: AAGTCGAAAATAAGAAAGAAATTATCTTCACATATGATGTTGACTTTCAGgcaagttctt ... atgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGC
EST: gi|124876845|gb|EH956282.1|EH956282
EST:     AGTCGAAAATAAGAAAGAAATTATCTTCACATATGATGTTGAACTTTCAG                         GAAAGTGAAGTGAAGTGGGCGTCTAGATG
genomic: AGTCGAAAATAAGAAAGAAATTATCTTCACATATGATGTTGA-CTTTCAGgcaagttctt ... atgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATG
EST: gi|86072801|gb|DR368558.1|DR368558
EST:     AAGTCGAAAATAAGAAAGAAATTATCTTCACATATGATGTTGACTTTCAG                         GAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGC
genomic: AAGTCGAAAATAAGAAAGAAATTATCTTCACATATGATGTTGACTTTCAGgcaagttctt ... atgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatactattgtgttcctgttctcactgttttgatttttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
                                              tgtcttc  CT-rich tract
                            ttttgattttt  TA-rich tract