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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaagagaatgtaacattgataaacaattcatttttggtgaggagcatatggtttaagatggtgtgtcgatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT

Basic information

species Arabidopsis thaliana
transcript AT5G17770.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 8
-tgcaaga-gaatgtaacattgataaacaattcatttttggtgaggagcatatggtttaagatggtgtgtc-gatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT
 || |    || | | |  ||  |   || |||| | |       ||   | |  | |    |  ||| ||  | || ||    ||| |  |    ||| |||||||| ||||| || || || || ||||||||||||||||||||| ||||||| |  ||    ||| |   ||||||||| |||||||||| | |    |
gtgaatcttgagtcttattttttttt-cagttcactatgaagatcgattgtgtattctctattcttgtatctaacctgagatgtgtttacct----atttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G422581_T01 (Zea mays), 3'ss of exon 3
-tgcaaga-gaatgtaacattgataaacaattcatttttggtgaggagcatatggtttaagatggtgtgtc-gatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT
 || |    || | | |  ||  |   || |||| | |       ||   | |  | |    |  ||| ||  | || ||    ||| |  |    ||| |||||||| ||||| || || || || ||||||||||||||||||||| ||||||| |  ||    ||| |   ||||||||| |||||||||| | |    |
gtgaatcttgagtcttattttttt---cagttcactatgaagatcgattgtgtattctctattcttgtatctaacctgagatgtgtttacct----atttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G127972_T01 (Zea mays), 3'ss of exon 3
-tgcaaga-gaatgtaacattgataaacaattcatttttggtgaggagcatatggtttaagatggtgtgtc-gatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT
 || |    || | | |  ||  |   || |||| | |       ||   | |  | |    |  ||| ||  | || ||    ||| |  |    ||| |||||||| ||||| || || || || ||||||||||||||||||||| ||||||| |  ||    ||| |   ||||||||| |||||||||| | |    |
gtgaatcttgagtcttattttttttttcagttcactatgaagatcgattgtgtattctctattcttgtatctaacctgagatgtgtttacct----atttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G076206_T01 (Zea mays), 3'ss of exon 5
-tgcaagagaat-gtaacattgataaacaattcatttttgg--------tgaggagcatatggtt-taagatggtgtgtcgatctaagtatggttcatgtttaa--attgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT
 || |  ||  |  |  | ||      || |||| | |  |        |||      |||  || || ||| || | |       | | |      ||||||   ||| ||||||||||| || || || ||  | ||||||||||||||||||||| ||||||| |  ||    ||| |   ||||||||| |||||||||| | |     
gtgaatcaggcttattgccttttctttcagttcactatgaggattgtcatgatttctctattcttgtatgattgtatctaacctggaatcttacatgtgtttacctatttcagATCCTAAGGTGTGGTCCTCCTTCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACGAAGGAGATGCAGTTCCAGTTCTAAGCAACGC

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
-----tgcaagagaatgtaa--cattgataaacaatt----catttt-tggtgaggagcatatggtttaagatggtgtgtcgatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT
     ||    |  || |||  ||||  |  | ||||     ||||| |  ||   | |||    |  |||   |      ||| ||    || ||| ||    | || |||||  | ||||| || ||||| || ||||||||||||||||||||| |||||||||| || |||||  || | |||||||| |||||||||||||     |
gtaattgtttcattatttaacccattactccaaaattatgatattttcttttgctaatcattgcataaaaggaagataaatgat-tagacgtgtttcttgcg-gattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 8
---------------------tgcaagagaatgtaacattgataaacaattcatttttggtgaggagcatatggtttaagatggtgtgtcgatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT
                       ||  |      ||   || ||     ||   ||||| |      ||| |     | || | |   |   |  | | ||   |   |    | || |||||  | ||||| || || || || ||||||||||||||||||||  |||||||||| || |||||  |||| |||||||| |||||||||||||     |
gtaattgtttcattatttaaccccattactccaaaattatgttatgatgttttcttttgctagttgtcatgtaaa--aggaagataaatgatttgacgcatttcttgcg---gattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT

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|86082325|gb|DR378084.1|DR378084
EST:     CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG                         ATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTT
genomic: CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAGgtataccctc ... taaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTT
EST: gi|125041609|gb|EL113878.1|EL113878
EST:     ATCTGATATTCAG                         ATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTT
genomic: ATCTGATATTCAGgtataccctc ... taaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTT
EST: gi|86066426|gb|DR362183.1|DR362183
EST:     CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG                         ATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTT
genomic: CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAGgtataccctc ... taaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTT
EST: gi|164056394|gb|EL972866.1|EL972866
EST:     CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG                         ATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCAT
genomic: CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAGgtataccctc ... taaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCAT
EST: gi|86066425|gb|DR362182.1|DR362182
EST:     CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG                         ATCCTAAGATGCGGAC-ACCGCC
genomic: CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAGgtataccctc ... taaattgcagATCCTAAGATGCGGACCACCGCC
EST: gi|164232482|gb|EL990866.1|EL990866
EST:     CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG                         ATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATG
genomic: CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAGgtataccctc ... taaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATG
EST: gi|86082753|gb|DR378512.1|DR378512
EST:     CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAG                         ATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTT
genomic: CAAAGGAAATGATTCAGACTCATTGCCCTGCACCTGCATCTGATATTCAGgtataccctc ... taaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatatggtttaagatggtgtgtcgatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT
                                     ttcatgtttaaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaagagaatgtaacattgataaacaattcatttttggtgaggagcatatggtttaagatggtgtgtcgatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- caagaga
- - - - - - - - - - -taaacaa
- - - - - - - - - - - - - - - - tttttgg