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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctctcttgctttcatttattagcttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT

Basic information

species Arabidopsis thaliana
transcript AT1G50480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
----------gttctctcttgctttcatttattagcttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgct-tagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT
            |   | ||   || |||| ||    ||     |||  |   || | || |  |||  ||  ||   |  || |    | ||||| |  | |||||||| ||||| || || ||||| |||||||| || || ||||||||||| || ||||| ||||| ||||| || || || || || || ||||||||||
gacatatcgatgtacatattatgtttattttttta--tagagtatatattatgttattgatatgctttactactttactcaatatt---aatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 2
--gttctctcttgctttcatttattagcttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgctta----gGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT
    | | |  |    | | ||   |   | |      |   ||||   |  ||  |     |  ||  ||  |||  ||| || |||||  |||    |||||| ||||| || || ||||| |||||||| || |||||||||||||| |||||||||||||| |||||||| || || || || || ||||||||||
catatgtgtgataaaataacttcagactgtcttgtaagtatctgctccagatcatgcggaagttgtttcatgtattaatgatgtattgttttttatgtagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACCTTTGGAATCAAGGGAGGTGCAGCTGGAGGTGGGTACAGCCAAGTTATACCCATGGATGAGT

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G13840.1 (Glycine max), 3'ss of exon 3
--------gttctctcttgctttcatttattagcttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT
         |    ||  | | | ||| |  | ||     ||| |  | |  | |  |     | ||   |   || |    | | |  | || ||| |||||| || || || ||||| ||||| || |||||||| || |||||||| ||||||||||||||||||||||| ||||| || || ||||| |||||||| |
ctggttatttgggttcaagatattattgaaaaactacaatctt-taatcgtatgtcaaagttatgctggatacataatcccatcttatctctttttg-ttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G44010.1 (Glycine max), 3'ss of exon 2
-gttctctcttgctttcatttattagc------ttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT
     | | | | ||  |  |||||         |||  |||    | |||| |  |     | ||   |   || |    | | |  | || ||| |||||| ||||| || ||||| ||||| || |||||||| || |||||||| |||||||| |||||||||||||| ||||| || || ||||| |||||||| |
caggttatttgggttcaagatattaatggaaaactataactttcaatcgcttgtcaaagttatgctggatacataatcccatcttatctctttttg-ttagGTAGTTACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGCGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 2
--------gttctctcttgctttcatttattagcttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT
         |    ||  | | | ||| |  | ||     ||| |  | || | |  |     | ||   |   || |    | | |  | || ||| |||||| || || || ||||| ||||| || |||||||| || |||||||| ||||||||||||||||||||||| ||||| || || ||||| |||||||| |
ctggttatttgggttcaagatattattgaaaaactacaatctt-taatcgcatgtcaaagttatgctggatacataatcccatcttatctctttttg-ttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT

upper sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
--gttctctcttgctttcattt-attagcttatgccttatgcttgc-ttttggacaaacttctctctttgtattgatttgtgaagtgttgttgct--tagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT
   |     | |  ||| |||| |  | |  |    |  || ||           |||  | |   ||  | |  || |      || |  || |  |||||||| || || ||||| ||||| ||||||||||| || |||||||| |||||||||||||| |||||||| || ||||| |||||||| ||||| ||||
gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT

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|301501774|gb|HO207314.1|HO207314
EST:     CTACCACTGTTGGACTTTGCCAAGCCTTAGGCGCTTACCTCGATAAGAAG                         GTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAA
genomic: CTACCACTGTTGGACTTTGCCAAGCCTTAGGCGCTTACCTCGATAAGAAGgttctctctt ... tgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAA
EST: gi|125301106|gb|EL315191.1|EL315191
EST:     CTACCACTGTTGGACTTTGCCAAGCCTTAGGCGCTTACCTCGATAAGAAG                         GTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAA
genomic: CTACCACTGTTGGACTTTGCCAAGCCTTAGGCGCTTACCTCGATAAGAAGgttctctctt ... tgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT
                           tattgat  putative branch site (score: 3)
                           tattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctctcttgctttcatttattagcttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG