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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatgaagtatttttgtacaaattctagttccatatgatactttatttgggaataacttaattgtcgtaagatattatttctctgtagTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATGGATGCAATATACTTCATCCAGCCAACTAAAGAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G12360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 3
-gtgagaatgaagtatttttgtacaaa-----ttctagttccatatgatacttt-atttgggaataacttaattgtcgtaagat-attatttctctgtagTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATGGATGCAATATACTTCATCCAGCCAACTAAAGAGAA
|||| | | | | |||| | | | | ||||| | || | | | |||| || || || || | ||| | || |||||| ||||| ||| || ||| || |||||| | |||||| ||||||| ||||| |||||||| ||||||||||||||
agtgatattcccatttctttggattgaagtgcctttgtgagaatatgggatttccactagatgctaacatagagtccgaaatatgaaaattgttttgcagTGGTCGAAGATTTATATAAACGGAGGCAACCATTGCCTTCACTGGATGCCATATATTTCATCCAACCAACTAAAGAGAA

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 4
gtgagaatgaa-gtatttttgtacaaattctagttccatatgatactttatttgg---gaataact-taattgtcgtaagatat----------tatttctctgtagTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATGGATGCAATATACTTCATCCAGCCAACTAAAGAGAA
|||| | ||| | | || || ||||||| | ||||| | | || | ||||| | ||| | ||| | | | | ||||||||||||||||||||| | ||||| |||||| | || | |||||||| |||||||||||||||||||| | ||||||
------atgattacactttcggaagaaaatta-ttccatagacacccatattttgctcaactagttctaattcttgtatggtatgtgatttgtttttctttttgtagTGGTTGAAGACATATTCAAGCGAAGGCAACCATTGCCCACCATGGATGCTATATACTTCATCCAGCCAACCAGAGAGAA

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 3
------------gtgagaatgaagtatttttgtacaaattctagttccatatgatactttatttgggaataacttaattgtcgtaagatattatt-tctctgtagTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATGGATGCAATATACTTCATCCAGCCAACTAAAGAGAA
| ||| || | || || | | | || | | || | ||| | || || | | || || | | |||||| ||||||||||||| | ||||| || ||| | || | ||||||| |||||||||||||||||||| | ||||||
tatgattacactttcggaagaaaattattccctagacacccatattttgcacaactagttct-----aattcttgtatgtatgtgatttgtttttctttttgtagTAGTTGAAGACATATACAAGCGAAGGCAGCCATTGCCCACCTTGGATGCTATATACTTCATCCAGCCAACCAGAGAGAA

upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 3
----gtgagaatgaagtatttttgtacaaattcta-gttccatatgatactttatttgggaataactt-aattgtcgtaagatattatttctctgt--agTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATGGATGCAATATACTTCATCCAGCCAACTAAAGAGAA
||| | || ||||| | || | || | || | | |||| | | | ||| | ||| || | ||||||||||| |||||| ||||| |||| | ||||| || ||| | || |||||||| |||||||||||||| |||||||| ||||||||
gtgtgtgtgtgtgtgtgttttttttttaatatatatataccttttttcgctttttcttttctcatctttgaatgtatcaaatttctatttctctgtgcagTGGTGGAAGATATATACAAGCGAAGGCAGCCATTGCCCTCAATGGACGCAATATACTTCATACAGCCAACCAAAGAGAA

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|164194439|gb|EL971670.1|EL971670
EST:     AATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT                         TGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATG
genomic: AATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCATgtgagaatga ... ttctctgtagTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatactttatttgggaataacttaattgtcgtaagatattatttctctgtagTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATGGATGCAATATACTTCATCCAGCCAACTAAAGAGAA
                                         ttatttctct  CT-rich tract
 taagatattatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaatgaagtatttttgtacaaattctagttccatatgatactttatttgggaataacttaattgtcgtaagatattatttctctgtagTGGTTGAAGACATATTTAGACGAAGACAACCACTTCCTTCAATGGATGCAATATACTTCATCCAGCCAACTAAAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA