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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctgtttatcattgcaaagtgattagtgaatcgattaacttggaactaatgggaatcaattttacatcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGA

Basic information

species Arabidopsis thaliana
transcript AT1G16180.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g54990.2 (Oryza sativa), 3'ss of exon 2
-----------------gtaa-gtttctgtttatcattgcaaa-gtgattagtgaatcgattaacttggaactaatgggaatcaattttacatcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGA
                  ||   |   | ||| | | || ||  |     |||    |   |  |  |    ||||   ||      ||   | ||||||| || || || ||||||||  ||||| | |||||||||||||| ||||| ||| | ||||| ||||||||||||||||| || |  ||||||| | | ||
ttttatatgctaattctatattatcagtttttgttactgtaattggagccagttctccccattccaggttgttaattttaactgtcatttgtttttgcagAATCAATATCCAAGTTTGGATCTGGACTGTTCCTGCTTGTTCAGGTTGTTCTTTTGTTGGACTTTGTTCATGGATGGAACGAGAATTGGGTTGCCAAGGA

upper sequence: AT1G16180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G46830.3 (Glycine max), 3'ss of exon 2
-----------------gtaagtttct--gtttatcattgcaaagtgattagtgaatcgattaacttggaactaatgggaatcaattttacatcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGA
                 ||  || | |  |    ||||    |  ||||  || ||| | || | |    |  | |  ||     | |  ||  |||||||  | || |||||||||||  | ||  | || || |||||||||||  | ||  | |||||||||||||||||||||||||||| ||||||||| || ||
atatgtatgtgtgatgtgtctgtctgtaggcccttcatatgcatttgatatgtaaattgtttcattgtttatgattttgatgaggtatgtcaatttgcagAAACAATATCAAAGTTTGGCTCGGGCATGTTTCTTCTTGTTCAAGTCATGCTCTTGTTGGATTTTGTTCATGGATGGAATGACAAATGGGTTGGATATGA

upper sequence: AT1G16180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G36750.1 (Glycine max), 3'ss of exon 2
----------------gtaagtttctgtttatcattgcaaa--gtgattagtgaatcgattaacttggaactaatgggaatcaatttta-catcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGA
                 |   ||    |||   ||| |     ||||| |    || | ||   |||    |  |    || |  | |  ||  |||||||  | || |||||||||||  | ||  | || || |||||||||||  | ||  | |||||||||||||||||||||||||||| ||||||||| |  ||
ccttttttgttgagctattgcttcgaatttgggattacttctcgtgatcaaattattgtttgtattgtttatggttttgatgaggtatgtcaatttgcagAAACAATATCAAAGTTTGGCTCAGGCATGTTTCTTCTTGTTCAAGTCATGCTCTTGTTGGATTTTGTTCATGGATGGAATGACAAATGGGTTGGATTTGA

upper sequence: AT1G16180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0018g01420.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtaagtttctgtttatcattgcaaagtgattagtgaatcgattaacttgga---actaa--tgggaatcaattttacatcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGA
               | || || ||||| |||||||   ||   |    ||    ||  |   ||   |||||  || |    || |||      ||||||| | |  |||||||| ||  | ||| | || || |||||||||||||| ||| | ||||||||||||||| |||||||||||||||||||||| || | 
gcactaaggtctcctttagattgtgtttttcattgctttgtttctttgaaaatttttctccacgattcactaagctgaggggtaagttttatggatgcagAGACAACATCAAAGTTCGGCTCAGGACTGTTTCTTCTTGTTCAAGTTGTGCTTTTATTGGATTTTGTTCATAGATGGAATGACACATGGGTTGGATATGG

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|125109508|gb|EL161928.1|EL161928
EST:     TGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATG                         AGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTAC
genomic: TGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATGgtaagtttct ... catcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTAC
EST: gi|164143102|gb|EL983208.1|EL983208
EST:     TTTAGTCATCTTTATGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATG                         AGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGC
genomic: TTTAGTCATCTTTATGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATGgtaagtttct ... catcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGC
EST: gi|125159319|gb|EL187458.1|EL187458
EST:     TTTAGTCATCTTTATGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATG                         AGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTAC
genomic: TTTAGTCATCTTTATGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATGgtaagtttct ... catcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTAC
EST: gi|125048692|gb|EL120961.1|EL120961
EST:     ATCATCAGTTTCTATG                         AGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTAC
genomic: ATCATCAGTTTCTATGgtaagtttct ... catcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTAC
EST: gi|163979673|gb|ES035996.1|ES035996
EST:     ATCTTTATGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATG                         AGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAAGTTGTA
genomic: ATCTTTATGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATGgtaagtttct ... catcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAA-GTTGTA
EST: gi|125029894|gb|EL102163.1|EL102163
EST:     GTTCTTCCTTCCAAATGAAATCATCAGTTTCTATG                         AGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTG
genomic: GTTCTTCCTTCCAAATGAAATCATCAGTTTCTATGgtaagtttct ... catcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTG
EST: gi|125160762|gb|EL188200.1|EL188200
EST:     TTTAGTCATCTTTATGTTCTTCCTTTCAAATGAAATCATCAGTTTCTATG                         AGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTAC
genomic: TTTAGTCATCTTTATGTTCTTCCTTCCAAATGAAATCATCAGTTTCTATGgtaagtttct ... catcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattagtgaatcgattaacttggaactaatgggaatcaattttacatcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGA
                        aactaat  putative branch site (score: 2)
                                  aatcaattttacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttctgtttatcattgcaaagtgattagtgaatcgattaacttggaactaatgggaatcaattttacatcttgcagAGTCGATGTCAAAGTTTGGTGCTGGATTTTTCCTGCTTGTTCAAGTTGTACTTCTTTTGGATTTTGTTCATGGATGGAATGACACATGGGTTGGCTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA