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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatctttctctgaccagaagctcgctgaagcgaaacttatgtaacctccttaatggtacttaattggcaaactgtttttgatgtttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAGCTTTGGCACGAAGAATTGGAGCCCCAAAACTCACTCTTAGACATTCTGA

Basic information

species Arabidopsis thaliana
transcript AT4G31300.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0065g00320.t01 (Vitis vinifera), 3'ss of exon 7
----gtaagatctttctctgaccagaagctcgctgaagcgaaacttatgtaacctccttaatggtacttaattggcaaactgtttttgatgtttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAGCTTTGGCACGAAGAATTGGAGCCCCAAAACTCACTCTTAGACATTCTGA
    |    |  |||   | | |  ||   |  |    |  ||   ||  |  | |  ||    || ||| |    ||    |  |||    | ||   ||||| ||||||||||| ||||||| |||||| |||||||| || |   | |   | |||||||| ||| |||||||||| ||||| ||  | |||||| |  
acttgcttcacatttacttcatctaaattgcattttgacttaaagaattaatacccactagc--tatttattatagaatgcatcattgtgtatgttctgcagATAAACTCAGAGGGGGTGACGAAAAACTTCTACCCTGGTGACACCCTTCCATTGTGGCACGAGGAACTGGAGCCCCAGAACTCTCTGCTGGACATTTTAT
















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|124887189|gb|EH966091.1|EH966091
EST:     CCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA                         ATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
genomic: CCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATAgtaagatctt ... ttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
EST: gi|116424148|gb|EG466740.1|EG466740
EST:     TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA                         ATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
genomic: TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATAgtaagatctt ... ttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
EST: gi|86074232|gb|DR369989.1|DR369989
EST:     TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA                         ATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
genomic: TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATAgtaagatctt ... ttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
EST: gi|125117854|gb|EL166813.1|EL166813
EST:     GGTGTCGTACGGACTGTCATA                         ATCAACTCTAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCA
genomic: GGTGTCGTACGGACTGTCATAgtaagatctt ... ttttgaacagATCAACTC-AGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCA
EST: gi|164177475|gb|EL974176.1|EL974176
EST:     GGAGCCAGTGGTGGTGTCGTACGGACTGTCATA                         ATCAACTCAGAGGGAGTGACGAGAA
genomic: GGAGCCAGTGGTGGTGTCGTACGGACTGTCATAgtaagatctt ... ttttgaacagATCAACTCAGAGGGAGTGACGAGAA
EST: gi|164216612|gb|ES189524.1|ES189524
EST:     TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA                         ATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGC
genomic: TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATAgtaagatctt ... ttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGC
EST: gi|47831542|gb|CK121226.1|CK121226
EST:     TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA                         ATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
genomic: TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATAgtaagatctt ... ttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
EST: gi|116444625|gb|EG487217.1|EG487217
EST:     TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATA                         ATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG
genomic: TAGCCATCGCCCGTGATGGAGCCAGTGGTGGTGTCGTACGGACTGTCATAgtaagatctt ... ttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaacctccttaatggtacttaattggcaaactgtttttgatgtttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAGCTTTGGCACGAAGAATTGGAGCCCCAAAACTCACTCTTAGACATTCTGA
                                          tgttttt  CT-rich tract
                                   tttttgatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatctttctctgaccagaagctcgctgaagcgaaacttatgtaacctccttaatggtacttaattggcaaactgtttttgatgtttttgaacagATCAACTCAGAGGGAGTGACGAGAAACTTTTACCCTGGAGATAAGTTGCAGCTTTGGCACGAAGAATTGGAGCCCCAAAACTCACTCTTAGACATTCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG