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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcctactgactactttgcgtaaatttcttatgcttggtatattcatttgagatttgaaatctactgaattctgaccaatgattctctcatcaaatctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G03650.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 6
gtatggcctactgactactt-tgcgtaaatttcttatgcttggtatattcatttgagatttgaaatctactgaattctgaccaatgattctctcatcaaatctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG
   ||   |  | |||| |  ||| |  |   ||  || |  |||  | ||| |||  || | ||  |  |   | | ||        | ||| ||  ||   ||  |||||||| ||||||||||||||||| ||| |||| |||||  ||||||| ||  || | ||||| ||||||||||||||||||
--ttgaggttgtaactaataatgcatggac--ctagtgtt--gtaattccatatga--ttggtaagttggtagttaccgatgctca--tatctaatgcaactgtttccagAATGAGTTTGGTGTTTGGGAGATTTTTCTGCCTAACAATGCTGATGGCTCATCTCCTATTCCACATGGCTCACGTGTAAAG

upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g33460.1 (Oryza sativa), 3'ss of exon 6
-gtatggcctactgactactttgcgtaaatttcttatgcttggtatattcatttgagatttgaaatctactgaattctgaccaatgattctctcatcaaatctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG
   |||    |  |  || || ||   |        |  ||   || | |     |  |||    |||  | | |  |||   |||      |||      ||||  |||||||| | ||||||||||||||| |   |||| |||||  ||||||| || ||||| ||||||||||||||||||||||||
gacatgaga-agggtgtatttcgcagcatacgagcctattta-catgtgccagcaacgttttttctcttattagtgttgatatatggcatgatca------cttt--cagAATGAGTATGGTGTTTGGGAGATTTCCCTGCCTAACAATGCTGATGGATCCCCTGCTATTCCTCATGGCTCACGTGTAAAG

upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 6
---gtatggccta--ctgactactttgcgtaaatttcttatgcttggtatattcatttgagatttgaaatctactgaattctgaccaatgattctctcatcaaatctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG
      || | ||  ||||| |  || | ||    | | |  |     || | ||||||| |  |    | |  |  || ||||   |||    | |||      ||||   ||||||| |  || ||||||||||| ||  |||| |||||  |||||||||| ||||| ||||||||||||||||||||||||
ttaacgtgacataagctgacgaggtttcata---ctatcaaac---acatttccatttgataagtatttttttatttatcctgatatatggaattatca------cttt--tagAATGAGTACGGCGTTTGGGAGATTTTCCTGCCTAACAATGCTGATGGTTCCCCTGCTATTCCTCATGGCTCACGTGTAAAG

upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G35020.2 (Glycine max), 3'ss of exon 6
gtatggcctactgactactttgcgtaaatttcttatgcttggtatattcatttgagatttgaaatctactgaattctgaccaatgattctctcatcaaatctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG
    ||   |  ||   |||| | | ||   ||||   ||  |  | | |||  |  |||  |  ||| ||          |||| ||||    |  |    || |||||||||||||||||| ||||||||||| ||||| |||||    |||||||| ||  ||||||||||||| || || || |||
----ggataatggatatctttacttgaa---cttaattttaattgact-attgtaattttttatcctattggcagtccttaaatg-ttctagttttgacaaattaacagAATGAATTTGGTGTGTGGGAGATCTTCTTGCCGAACAATGTGGATGGTTCACCACCAATTCCTCATGGTTCTCGGGTCAAG

upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G37750.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------------------------gtatggcctactgactactttgcgtaaatttcttatgcttggtatattcatttgagatttgaaatctactgaattctgaccaatgattctctcatcaaatct----ttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG
                                                                                       ||       |||  |  ||| |       |||   |||  |   |   ||||| |  || ||  |  |    | |   || |  ||   |  || | | |    || |||||||||||||||||| ||||||||||| ||||| |||||    |||||||| ||  ||||||| ||||| || || || |||
gtatgttatccttaattggtctttaaagttcatacatgtgaaattcagcatacttctttcattaataagcccttatatcatatgtaaataaaaagttgaacatattgtggtttcaacttcctcttttttcctctgtttgacaactgtaaatttttatcctattggcagtctttaaatgttctagttttgacttaacagAATGAATTTGGTGTGTGGGAGATCTTCTTGCCAAACAATGTGGATGGTTCACCACCAATTCCCCATGGTTCTCGGGTCAAG

upper sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 6
gtatggcctactgactactttgcgtaaatttcttatgcttggtatattcatttgagatttgaaatctactgaattctgaccaatgattctctcatcaaatctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG
     ||    |   |  |||  ||    | |||    ||  ||||    ||  | || |  |||  |   ||  |      |  ||||  | || |  || |  |||||||||||||||||| ||||||||||||||||| |||||  | |||||||| ||| |||| || |||||||| || || |||
-----gcactttactttttttatgttg--tgcttggaatta-tataccagttcaatatctttaattaatctaacacaataataaaattcattgattat-tcatgaacagAATGAATTTGGTGTGTGGGAGATCTTTTTGCCAAACAATGCAGATGGTTCACCTCCAATCCCCCATGGCTCTCGAGTGAAG

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|116483369|gb|EG525961.1|EG525961
EST:     TTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATCATGACTCGG                         AATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACAC
genomic: TTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATCATGACTCGGgtatggccta ... tctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACAC
EST: gi|116412441|gb|EG455033.1|EG455033
EST:     TTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATCATGACTCGG                         AATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCG
genomic: TTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATCATGACTCGGgtatggccta ... tctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttgaaatctactgaattctgaccaatgattctctcatcaaatctttgacagAATGAATTTGGTGTTTGGGAGATCTTTTTGCCCAACAACACTGATGGTTCGCCTGCAATTCCTCATGGCTCACGTGTAAAG
                   ttctgac  putative branch site (score: 2)
                                             tcttt  putative PPT
                                          aaatcttt  TA-rich tract