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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGTTTGGATGTTGATGCCCTCTTCATATCACACATCCAAGTGAACCAGGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttgagattttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G67430.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv01s0010g03380.t01 (Vitis vinifera), 5'ss of exon 4
AAAGGTTTGGATGTTGATGCCCTCTTCATATCACACATCCAAGTGAACCAGGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttgagattttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttg-cag
|||||| ||||||||||| | |||| |||||| ||||||||||||||||||||    || |||||| |  | || ||||| ||||| ||||||||||||||||||||||     ||  |||||    |  |   ||  |  ||||  |||    | | |    |    |  |  ||| ||| |||
AAAGGTCTGGATGTTGATTCACTCTACATATCTCACATCCAAGTGAACCAGGCACAGAAACAAAGGCGCCGCACATACCGGGCTCATGGAAGAATCAACCgtaagtttgtttcctttcaaatctagcatttgtgtaa-tggttgttttcctaaatgttaacaggaaccttctatttgtttggcag

upper sequence: AT1G67430.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv01s0010g03370.t01 (Vitis vinifera), 5'ss of exon 6
AAAGGTTTGGATGTTGATGCCCTCTTCATATCACACATCCAAGTGAACCAGGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttgagattttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttg-cag
|||||| ||||||||||| | |||| |||||| ||||||||||||||||||||    || |||||| |  | || ||||||||||| ||||||||||| |||| |||||     ||  ||||   |  | ||  |   |  | ||  |||    | |   |  |    |  |  ||| ||| |||
AAAGGTCTGGATGTTGATTCACTCTACATATCTCACATCCAAGTGAACCAGGCACAGAAACAAAGGCGCCGCACATACCGTGCTCATGGAAGAATCAATCgtatgtttgtttcctttcaaatttat--cttttgtgtatggtcgttttcctaaatgttgataggagccttctatttgtttggcag
















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|164220296|gb|ES020364.1|ES020364
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|164118238|gb|EL983017.1|EL983017
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCC
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCC
EST: gi|163991518|gb|ES074750.1|ES074750
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATG
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATG
EST: gi|164099880|gb|EL971382.1|EL971382
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTG
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTG
EST: gi|164190626|gb|ES125125.1|ES125125
EST:     GCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: GCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|164039243|gb|ES154020.1|ES154020
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACA
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACA
EST: gi|125042829|gb|EL115098.1|EL115098
EST:     CGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: CGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|164213923|gb|ES183351.1|ES183351
EST:     CACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: CACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|125271846|gb|EL285931.1|EL285931
EST:     AGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCTAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAA
genomic: AGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCC-AACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAA
EST: gi|125000168|gb|EL072437.1|EL072437
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCA
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCA
EST: gi|164134259|gb|EL981474.1|EL981474
EST:     GGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTC
genomic: GGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTC
EST: gi|164097057|gb|ES174331.1|ES174331
EST:     GCCGCAAAGACAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACA
genomic: GCCGCAAAG-CAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACA
EST: gi|124961665|gb|EL036166.1|EL036166
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTG
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTG
EST: gi|124881951|gb|EH960853.1|EH960853
EST:     GACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: GACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|164236323|gb|EL984694.1|EL984694
EST:     GAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: GAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|164128696|gb|ES149348.1|ES149348
EST:     AAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: AAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|125236946|gb|EL251031.1|EL251031
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGG
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGG
EST: gi|116451520|gb|EG494112.1|EG494112
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|124807339|gb|EH893743.1|EH893743
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCCAACCCA
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCC-AACCCA
EST: gi|164115089|gb|ES044490.1|ES044490
EST:     AAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTG-CAGAGAAGGAAG
genomic: AAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|164149072|gb|ES144576.1|ES144576
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         TTTACATGTCCAACCCAT
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCAT
EST: gi|124735667|gb|EH827069.1|EH827069
EST:     CAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: CAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|164181624|gb|ES123856.1|ES123856
EST:     CAAAGCAAAGGAGAAGGACTTACCGTGCTCTACGGTAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: CAAAGCAAAGGAGAAGGACTTACCGTGCTC-ACGG-AAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|163994899|gb|ES155865.1|ES155865
EST:     GCCGC-AAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACA
genomic: GCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACA
EST: gi|125063567|gb|EL131500.1|EL131500
EST:     GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: GGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
EST: gi|124975864|gb|EL049325.1|EL049325
EST:     AGAAGGACTTACCGTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAAGAGAAGGAA
genomic: AGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCA-GAGAAGGAA
EST: gi|124978421|gb|EL051601.1|EL051601
EST:     GCCGCAAAGCAAAGGAGAAGGACTTACCGTTGCTCACGGAAGAATCAACC                         CTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG
genomic: GCCGCAAAGCAAAGGAGAAGGACTTACCG-TGCTCACGGAAGAATCAACCgtaagtttga ... ttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGTTTGGATGTTGATGCCCTCTTCATATCACACATCCAAGTGAACCAGGCCGCAAAGCAAAGGAGAAGGACTTACCGTGCTCACGGAAGAATCAACCgtaagtttgagattttgtaaatcacttacattgatagctttttgtaatccattgtatgactcagtttgtctttcttggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA