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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaatctgaaactccttgaagaagagttttggattatgaattctgttgtgaaagtgttaaattatgtgccctgatgtcctatgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAAGGCTAGAATTTTATGACAAAGGTGTTGCCCCACGCAAGAACGTGGATGT

Basic information

species Arabidopsis thaliana
transcript AT1G56110.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g46720.1 (Oryza sativa), 3'ss of exon 6
gtaaaaatctgaaactccttgaagaagagttttggattatgaattctgttgtgaaagtgttaaattatgtgccctgatgtcctatgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAAGGCTAGAATTTTATGACAAAGGTGTTGCCCCACGCAAGAACGTGGATGT
     | |    ||||   | |  | |  ||    ||  | | || | |  |  | || ||   | || ||        | | |      | |   | || | | ||| ||| ||||||| ||||||||||||||||| || ||||| || |||||||| ||| |||| || || |||||| | |||||
--gttagttgagaactttgttagcatgctttacacatggtta-ttatctgatctatgtttttc-tcatttgattgtggattcca---gAGTTGAATACCT-CAGTTTTCGGTCAGAAGCTGCGCGAACAAGTTGAGGAGAGACTAGACTTCTATGACAAGGGTATTGCACCGCGTAAGAACCTTGATGT

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 6
--gtaaaaatctgaaactc-cttgaagaagagttttggattatgaattctgttgtgaaagtgttaaattatgtgccctgatgtcctatgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAAGGCTAGAATTTTATGACAAAGGTGTTGCCCCACGCAAGAACGTGGATGT
   |     | | | | || ||| |  || |  |   |  | |  ||     | ||  |   || |  | ||| ||   |||       ||||  | |  ||||||| |||||| ||||| || || || |||||||||||| | || || ||||||||||| || |||||||| ||||||||| | |||||
gtttgtttctttcatattcactttagcaatatctcatggctgtacatagcactttgtcatgatttagctttgtacctcaatg-------cagAAAGGGGTACTACTGTTTTTGGGGAGAAACTGCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT

upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 6
gtaaaaatctgaaactccttgaagaagagttttggattatgaattctgttgtgaa-agtgttaaattatg-tgccctgatgtccta-tgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAAGGCTAGAATTTTATGACAAAGGTGTTGCCCCACGCAAGAACGTGGATGT
       | ||    | |||| | |     ||| |  |||    |  | |||  | ||   |   | ||| |    || | || || ||||||    |  ||||||| ||||||  |||| || || || |||||||||||| | || || ||||||||||| || |||||||| ||||||||| | |||||
------gtttg---tttcttgcatattcactttagcatatttcatg-gctgtacatagccctttgtcatgattttgtggtatcttaatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT

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|124718462|gb|EH809864.1|EH809864
EST:     TCTTGCAAACAAGTGCTCTATAGCATCCCGGATTGATTGTTTTGCTG                         ATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAA
genomic: TCTTGCAAACAAGTGCTCTATAGCATCCCGGATTGATTGTTTTGCTGgtaaaaatct ... tcctatgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAA
EST: gi|125030365|gb|EL102634.1|EL102634
EST:     TCCCGGATTGATTGTTTTGCTG                         ATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAA
genomic: TCCCGGATTGATTGTTTTGCTGgtaaaaatct ... tcctatgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatgaattctgttgtgaaagtgttaaattatgtgccctgatgtcctatgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAAGGCTAGAATTTTATGACAAAGGTGTTGCCCCACGCAAGAACGTGGATGT
                                     ccctgat  putative branch site (score: 4)
                   aaagtgttaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatctgaaactccttgaagaagagttttggattatgaattctgttgtgaaagtgttaaattatgtgccctgatgtcctatgcagATGGTGCAACTACTGCTTTTGGTGAGAAGCTTCGCGAACAAGTTGAGGAAAGGCTAGAATTTTATGACAAAGGTGTTGCCCCACGCAAGAACGTGGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC