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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaaaacctgtgcttaaattgtctctaatttgaatttatgaattggtctcccttatctaccattatgtcctgcagaatcatcaaacatcatgtgaacttacttatcaatgagctgttaataacgctgtgtttccctggtttattggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGACATTAAAGCGTTTTGTAAGAAGAATTTGGCAGCTTTCAAGGTGCCAAAGA

Basic information

species Arabidopsis thaliana
transcript AT3G48990.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g03660.t01 (Vitis vinifera), 3'ss of exon 3
gtaaacaaaacctgtgcttaaattgtctctaatttgaattta-tgaattggtctcccttatctaccattatgtcctgcagaatcatcaaacatcatgtgaacttacttatcaatgagctgtta-ataacgctgtgtttccctggtttattggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGACATTAAAGCGTTTTGTAAGAAGAATTTGGCAGCTTTCAAGGTGCCAAAGA
                                   |||   | |  |||| |   |  | | || |||||  |     | || ||   |  |         |||   | |   |||  ||||| |    |||    ||   | |||||||  | | |||||| || || ||  | ||||| ||||||||  ||    |   ||||   ||  |      |||||| ||||||||||||||| |||||||||| |||||||
------------------------------gtacggaacccactctattgattatcaat-tttatcattacct-----aaaaacagggatgaaagaaaaggcttgtgtgtt--tgaaatgttacagtgtgctaatcttggttcgtttattcatat-tcagATAAATTGCGCCATAATTCCTAGAGAAGGGTCTGACTTGGACGAATCAGAGGTGCTGCGGTTTTGCAAGAAGAATTTGGCAACTTTCAAGGTTCCAAAGA
















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|301501756|gb|HO207296.1|HO207296
EST:     TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAG                         ATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
genomic: TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
EST: gi|125326749|gb|EL340829.1|EL340829
EST:     AGAAATATGGGGAAGAG                         ATTAACTGTGCGGTTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGA
genomic: AGAAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGG-TGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGA
EST: gi|116467688|gb|EG510280.1|EG510280
EST:     TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAG                         ATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
genomic: TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
EST: gi|116467687|gb|EG510279.1|EG510279
EST:     TTTTTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAG                         ATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
genomic: TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
EST: gi|125106712|gb|EL160101.1|EL160101
EST:     AAATATGGGGAAGAG                         ATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
genomic: AAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
EST: gi|86081105|gb|DR376862.1|DR376862
EST:     TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAG                         ATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
genomic: TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
EST: gi|116483995|gb|EG526587.1|EG526587
EST:     TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAG                         ATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
genomic: TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
EST: gi|116464394|gb|EG506986.1|EG506986
EST:     TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAG                         ATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAGGAGGAC
genomic: TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC
EST: gi|116464272|gb|EG506864.1|EG506864
EST:     TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAG                         ATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAGGAGGAC
genomic: TTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGAAGAGgtaaacaaaa ... ggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttatcaatgagctgttaataacgctgtgtttccctggtttattggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGACATTAAAGCGTTTTGTAAGAAGAATTTGGCAGCTTTCAAGGTGCCAAAGA
                 taataac  putative branch site (score: 1)
              tgttaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacaaaacctgtgcttaaattgtctctaatttgaatttatgaattggtctcccttatctaccattatgtcctgcagaatcatcaaacatcatgtgaacttacttatcaatgagctgttaataacgctgtgtttccctggtttattggtttatcagATTAACTGTGCGGTGATTCCAAGAGAAGGAACTACTGTAACCGAAGAGGACATTAAAGCGTTTTGTAAGAAGAATTTGGCAGCTTTCAAGGTGCCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT