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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaacgacttgcttctcctcgatttctctatgactctgttacatagcgctctaataaaatggtctgaaacggaattatgggaactacag

Basic information

species Arabidopsis thaliana
transcript AT1G78900.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 19
GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaacgacttgcttctcctcgatttctctatgactctgttacatagcgctctaataaaatggtctgaaacggaattatgggaactacag
|| || ||||| | ||||||    || ||||| |||||  | ||||| ||||||||||||||  | |||||||| |||||||| ||||||| || ||  |   |||| | | | |||   | | |     ||| |  | | |   || |    || ||||   |   |||   |         
GCAGTAGAGAGGGGAGCTGGTTCAGATGGTCAGAAGATATCTTACACCCTTATCAAGCATCGTATGGGAGATCTGTTCTACCGATTAGTgtgagtaattgtagtgctacac-tagatacttattttgacatgtaaagtgg-gtcttattctgttgatctgttgcc--attgcag---------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 19
GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaacgacttgcttctcctcgatttctctatgactctgttacatagcgctctaataaaatggtctgaaacggaattatgggaactacag
|| || ||||| | ||||||    || ||||| |||||  | ||||| ||||||||||||||  | |||||||| |||||||| ||||||| || |   |   |||| | |    |  |   | ||||  ||| |  | | | | || |    || ||||    |  |||   |         
GCAGTAGAGAGGGGAGCTGGTTCAGATGGTCAGAAGATATCTTACACCCTTATCAAGCATCGTATGGGAGATCTGTTCTACCGATTAGTgtgagtagttgtagtgctacactagaaacttattttgaca-tgtaaagtgg-gttttattctgttgatctgt--tgtcattgcag---------

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 19
GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaacgacttgcttctcctcgatttctctatgactctgttacatagcgctctaataaaatg-gtctgaaacgg---aattatgggaactacag
|| || ||| | | |||||| ||||| || || ||||| || ||||| |||||||||||||| || |||||||| ||||| ||| | |||||||  ||  | |  | | |   | |   |   |          |  |     | |||  ||    |||| || | |   |  |||    |||||||
GCAGTAGAGCGTGGAGCTGGTATGGATGGACAGAAGATAACTTACACCCTTATCAAGCATCGGTTGGGAGATCTGTTCTATCGTCTTGTgtaagtgaa--attgccatgttaacaaagacaaaagatgaactgcatgtgagattttaaggaagcatgtcttaatcagctcatatatctacactacag

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|116484152|gb|EG526744.1|EG526744
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116484817|gb|EG527409.1|EG527409
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116423655|gb|EG466247.1|EG466247
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116423878|gb|EG466470.1|EG466470
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTTTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116423877|gb|EG466469.1|EG466469
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116467266|gb|EG509858.1|EG509858
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|125059308|gb|EL127985.1|EL127985
EST:     TCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGTACCCAGTCAGAAGGGGAGGATACACTGGTGGAA
genomic: TCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAG-ACCCAG-CAGAAGGGGAGGATACACTGGTGGAA
EST: gi|116484141|gb|EG526733.1|EG526733
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116452176|gb|EG494768.1|EG494768
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|86077026|gb|DR372783.1|DR372783
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGARAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116436722|gb|EG479314.1|EG479314
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116424281|gb|EG466873.1|EG466873
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116452175|gb|EG494767.1|EG494767
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116456041|gb|EG498633.1|EG498633
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116433583|gb|EG476175.1|EG476175
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|124721513|gb|EH812915.1|EH812915
EST:     GAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: GAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116423654|gb|EG466246.1|EG466246
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116451304|gb|EG493896.1|EG493896
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116424219|gb|EG466811.1|EG466811
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
EST: gi|116468179|gb|EG510771.1|EG510771
EST:     ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGT                         GTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA
genomic: ACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaac ... ggaactacagGTCTCAGAAGTTCGAAGACCCAGCAGAAGGGGAGGATACACTGGTGGAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGTTGAGAGAGCAGCTGGAATGGACGGTCAAAAGATTACCTACACTCTTATCAAGCATCGCTTAGGAGATCTTTTCTACCGTTTAGTgtaagcaaacgacttgcttctcctcgatttctctatgactctgttacatagcgctctaataaaatggtctgaaacggaattatgggaactacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC