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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcattaaactagattgggtgttgtgaatgtcacctgatcactgatcaaaatgtcttccaaatgataactttccttaggcaaatccatatgtatggtggagatatagttgtatgtttaagagaagcagtttttaatgcatgttctaatgtttctgttatttggtttaacagGGAGCATTTATTGATCAGCACTTTGATCATGACTTGAACTTTTATGCTACAGAGGAAGACACCGTTAGTGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G25840.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25840.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 10
gttagcattaaactagattgggtgttgtgaatgtcacctgatcactgatcaaaatgtcttccaaatgataactttccttaggcaaatccatatgtatggtggagatatagttgtatgtttaagagaagcagtttttaat-gcatgttctaatgttt---ctgttatttggtttaacagGGAGCATTTATTGATCAGCACTTTGATCATGACTTGAACTTTTATGCTACAGAGGAAGACACCGTTAGTGGAAAG
                                                                             |||      |  ||||||   ||   | |  | ||  ||  |  | | ||    | | |||| || |    || | |||   || || |||  | | |||||||||||||| |||||||||||||||||| ||| | || ||  |||| || ||||| ||  | || |     |||
-----------------------------------------------------------------------------ttacatttgtatatatgttctgtatggctgca-ttacattgtggatataattcttctctaattgctttgaatattttttgctcttttctttcttcttacagGGAGCATTTACTGATCAGCACTTTGATCAGGACCTTAATTTCCATGCCACTGAGGAGGATCCTGTCACAAAGAAG
















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|124934331|gb|EL011410.1|EL011410
EST:     GCCTTCATATGGAACTGAAAGGTCCCTTCCCTAAAAAGATGCTTCGCAAG                         GGAGCATTTATTGATCAGCACTTTGAT
genomic: GCCTTCATATGGAACTGAAAGGTCCCTTCCCTAAAAAGATGCTTCGCAAGgttagcatta ... ggtttaacagGGAGCATTTATTGATCAGCACTTTGAT
EST: gi|125293080|gb|EL307165.1|EL307165
EST:     GCCTTCATATGGAACTGAAAGGTCCCTTCCCTAAAAAGATGCTTCGCAAG                         GGAGCATTTATTGATCAGCACTTTGATCATGACTTGAACTTTTATGCTA
genomic: GCCTTCATATGGAACTGAAAGGTCCCTTCCCTAAAAAGATGCTTCGCAAGgttagcatta ... ggtttaacagGGAGCATTTATTGATCAGCACTTTGATCATGACTTGAACTTTTATGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagagaagcagtttttaatgcatgttctaatgtttctgttatttggtttaacagGGAGCATTTATTGATCAGCACTTTGATCATGACTTGAACTTTTATGCTACAGAGGAAGACACCGTTAGTGGAAAG
                         ttctaat  putative branch site (score: 2)
          agtttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcattaaactagattgggtgttgtgaatgtcacctgatcactgatcaaaatgtcttccaaatgataactttccttaggcaaatccatatgtatggtggagatatagttgtatgtttaagagaagcagtttttaatgcatgttctaatgtttctgttatttggtttaacagGGAGCATTTATTGATCAGCACTTTGATCATGACTTGAACTTTTATGCTACAGAGGAAGACACCGTTAGTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA