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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTATGTTGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctattgagttcacagtttctgtgagattctcgtaagcatgttgatgagcttaacttggtagagtagttagcatgctgaatcatgtagtgttgatt...

Basic information

species Arabidopsis thaliana
transcript AT4G14210.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14210.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 5'ss of exon 7
----AAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTATGTTGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctattgagttcacagtttctgtgagattctcgtaagcatgttgatgagcttaacttggtagagtagttagcatgctgaatcatgtagtgttgatt---
    ||||||||| |||||||||||||||| ||||| || || || ||||||||||| || |||||||||||  | ||    || |||||| ||||||||| |  || | |    |  |||     | ||| |  |    ||   || |   |      || ||   ||   | |   | ||   | |  | ||  |||    |   
GGTGAAGTTTGCTCTTGGACTTTTGCCAGCAATGGTTGGTGGCCAAGCTTATGTTGAAGCTCAAGATGGTTTTACTGTTTCTGAGTGGATGAAAAAGCAGgta--taagttcacaatatcag----tttgtcaagtctctgtgtacaagac-acatttctacctcattaatttggaatggatataggagaaggtgttgtaagctaga

upper sequence: AT4G14210.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 6
----AAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTATGTTGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctattgagttcacagtttctgtgagattctcgtaagcatgttgatgagcttaacttggtag--agtagttagcatgctgaatcatgtagtgttgatt
    || ||||| ||||| ||| | ||||| ||| | || || ||| | ||||||||||| ||||||||| | |||||  ||||||||||| ||||||||| |       | |   | |    ||  |  |   | ||   |||     || |  | |||  ||   |    |||  |  || | ||| | | |  |   |||   
AGTCAAATTTGCAATTGGGCTTCTACCAGCTATGCTTGGTGGACAGCCATATGTTGAGGCTCAAGATGGTCTTTCAGTTCAAGAATGGATGAAAAAGCAGgtatagcacttttcttgattgt-gtaaccttagcagtccattaatagatttaagtaacttggctatatcaccagtcatgggc-tactgcaacttaaaa-attg---

upper sequence: AT4G14210.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA18G00720.2 (Glycine max), 5'ss of exon 2
----AAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTATGTTGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctattgagttcacagtttctgtgagattctcgtaagcatgttgatgagcttaacttggtagagtagtta--gcatgctgaatcatgtagtgttgatt
    || ||||| ||||| ||| | ||||| ||| | ||||| ||| | ||||||||||| ||||||||| | || ||  ||||||||||| ||||||||| |       | |   | |    ||  |  |   | ||   |||     || |  | |||  ||   |  |  ||| |  || | |||   | |  |   |||   
AGTAAAATTTGCAATTGGGCTTCTCCCAGCTATGCTTGGCGGACAGCCATATGTTGAGGCTCAAGATGGTCTTTCTGTTCAAGAATGGATGAAAAAGCAGgtatagcacttgtcttgattgt-gtaaccttagcagtccattaatagatttaagtaacttggctatatc-accagtcatggcctactgcgacttaaaa-attg---

upper sequence: AT4G14210.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 7
----AAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTATGTTGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctattgagttcacagtttctgtgagattctcgtaagcatgttgatgagcttaacttggtagagtagttagcatgctgaatcatgtagtgttgatt
    |||||||||||||||||| ||||||| ||| |||| || |||||||||||||| || || ||||||||| | || ||||| ||||||  ||| || | | |   | | ||| | | |   | | |   || |||  || |   | | | |||   ||  |    |  | || ||   |   | | | |||    ||    
AATCAAGTTTGCTATTGGACTTGTGCCAGCAATGCTCGGAGGACAGGCTTATGTTGAAGCACAGGATGGTTTAACTGTTAAAGACTGGATGAGAAAACAAgtatggctgttgttgtgataatgctctattgcaggttcatgttaagttctgggtgaagcta-ttgaacaatgaagctaagcttgagcagcttgtgaatttt---

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|86074021|gb|DR369778.1|DR369778
EST:     CAAAGAATGGATGGAAAAGCAGGGAG                         TACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
genomic: CAAAGAATGGATGGAAAAGCAGGCAAgtaggctatt ... gtccagggagTACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
EST: gi|86074020|gb|DR369777.1|DR369777
EST:     CAAAGAATGGATGGAAAAGCAGGGAG                         TACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
genomic: CAAAGAATGGATGGAAAAGCAGGCAAgtaggctatt ... gtccagggagTACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
EST: gi|86074019|gb|DR369776.1|DR369776
EST:     CAAAGAATGGATGGAAAAGCAGGGAG                         TACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
genomic: CAAAGAATGGATGGAAAAGCAGGCAAgtaggctatt ... gtccagggagTACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
EST: gi|86074018|gb|DR369775.1|DR369775
EST:     CAAAGAATGGATGGAAAAGCAGGGAG                         TACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
genomic: CAAAGAATGGATGGAAAAGCAGGCAAgtaggctatt ... gtccagggagTACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
EST: gi|116473797|gb|EG516389.1|EG516389
EST:     TGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGGAG                         TACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
genomic: TGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctatt ... gtccagggagTACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCATGTCAAAGGCGCTAA
EST: gi|125244532|gb|EL258617.1|EL258617
EST:     TGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGGAG                         TACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCAT
genomic: TGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctatt ... gtccagggagTACCTGAGCGCGTGACCGACGAGGTGTTTATTGCCAT
EST: gi|125199065|gb|EL214019.1|EL214019
EST:     TGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGGAG                         TACCTGAGCGCGTGACCGACGAGG
genomic: TGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctatt ... gtccagggagTACCTGAGCGCGTGACCGACGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTTTGCTATTGGACTTTTGCCAGCCATGGTCGGCGGTCAGGCTTATGTTGAGGCCCAAGATGGTTTATCAGTCAAAGAATGGATGGAAAAGCAGGCAAgtaggctattgagttcacagtttctgtgagattctcgtaagcatgttgatgagcttaacttggtagagtagttagcatgctgaatcatgtagtgttgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA