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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgtactcttatcattccgcaattccatggctaataaaaatacattgactggttctgaaacagagcattgacactgttttataaattacagGTGGCTACTGATGTTGCAGCAAGAGGGCTTGATATCCCGGACGTGGAAGTTGTGATAAACTACACTTTCCCTTTAACAACAGAGGATTATGTACACAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G31970.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31970.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv02s0109g00380.t01 (Vitis vinifera), 3'ss of exon 12
---gtatgcgtactcttatcattccgcaattccatggctaataaaaatacattgactgg--ttctgaaacagagcattgacactgttttataaat-tacagGTGGCTACTGATGTTGCAGCAAGAGGGCTTGATATCCCGGACGTGGAAGTTGTGATAAACTACACTTTCCCTTTAACAACAGAGGATTATGTACACAGAA
     |   || ||   |||| | |    |   ||   |        | ||      |   ||   ||  |   |||| |   || |||||   | | ||| | ||||| ||||| || ||| ||||  | ||||| || || |||||||| ||||| ||||||| ||| ||| | || |||||||||||||| |||||||
aattaaaatgttctaagatcactgctggttattatattttgagtccttgcaagagtggaaattgcaaagtatgacatttat-ttgctttatgtttgtgcagATAGCTACAGATGTGGCTGCACGAGGATTGGATATTCCAGATGTGGAAGTAGTGATCAACTACAGTTTTCCTCTCACTACAGAGGATTATGTTCACAGAA
















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|124705016|gb|EH796418.1|EH796418
EST:     TTCAAAGAAGGATCCTGCCCGTTACTG                         GTGGCTACTGATGTTGCAGCAAGAGGGCTTGATATCCCGGACGTGGA
genomic: TTCAAAGAAGGATCCTGCCCGTTACTGgtatgcgtac ... taaattacagGTGGCTACTGATGTTGCAGCAAGAGGGCTTGATATCCCGGACGTGGA
EST: gi|164217790|gb|ES092384.1|ES092384
EST:     AACGTACCAGGTCTTTATCATTGTTCAAAGAAGGATCCTGCCCGTTACTC                         GTGGCTACTGA
genomic: AACGTACCAGGTCTTTATCATTGTTCAAAGAAGGATCCTGCCCGTTACTGgtatgcgtac ... taaattacagGTGGCTACTGA
EST: gi|164036031|gb|ES113028.1|ES113028
EST:     AACGTACCAGGTCTTTATCATTGTTCAAAGAAGGATCCTGCCCGTTACTC                         GTGGCTACTGA
genomic: AACGTACCAGGTCTTTATCATTGTTCAAAGAAGGATCCTGCCCGTTACTGgtatgcgtac ... taaattacagGTGGCTACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatacattgactggttctgaaacagagcattgacactgttttataaattacagGTGGCTACTGATGTTGCAGCAAGAGGGCTTGATATCCCGGACGTGGAAGTTGTGATAAACTACACTTTCCCTTTAACAACAGAGGATTATGTACACAGAA
                             cattgac  putative branch site (score: 3)
                                    actgttttataaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgtactcttatcattccgcaattccatggctaataaaaatacattgactggttctgaaacagagcattgacactgttttataaattacagGTGGCTACTGATGTTGCAGCAAGAGGGCTTGATATCCCGGACGTGGAAGTTGTGATAAACTACACTTTCCCTTTAACAACAGAGGATTATGTACACAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT