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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcatcattaccttgttcttattaggtttcttgtaacctgcatcaagttagcaactttcttttgagtttgaccggttgctggtttgtatggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA

Basic information

species Arabidopsis thaliana
transcript AT1G59900.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 2
gtgcatcattaccttgttcttattaggtttcttgtaacctgcatcaagttagcaactttcttttgagtttgaccggttgctggtttgtatggataa-acagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA
 ||||  |     | |   |    |||  |   |    | |  |            ||   |    ||      ||||   |     | ||  |    ||||| |||||||||||||   |||| |||||||||||||| |||||||| ||||| |||||  | || || || || || 
-tgcaagaagttatggggatatgcaggcatggaggtggccgtgttggtgctcttgtttgtatcgttgtgatgatggttatggtaccttgtgtttggtgcagGTCGATGGTATGGATGTTCTTGCAGTCAAACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 2
-----gtgcatcattaccttgttcttattaggtttcttgtaacctgcatcaagttagcaactttcttttgagtttgaccggttgctggtttgtatggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA
     |   |||  |||   | | | ||||  | |    ||    | |     || | |   |  |||| | |||   |   ||    ||| ||    |  |||||| |||||||||||||   ||||||| |||||||||||||||||||| ||| | ||||| ||| |||| || ||  | 
tgtctgcatatctatacacaggt-taattaaatatac-atagtaagtagtctttttgaacaatcttttttaattt--tcaaatgaatatttatactt-tgtacagGTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 2
--gtgcatcattaccttgttcttattaggtttcttgtaacctgcatcaagttagcaactttcttttgagtttgaccggttgctggtttgtatggat-aaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA
   |     ||   | ||| || |||   | | |||||  ||   |   || | | || || |||  | |||    ||  |    | | |||   |    ||||||||||| ||||||||  ||||||| ||||||||||| |||||||| ||| ||  ||| ||| |||| || || || 
agctatgatatatacatgtgctgattgaatgtgttgtagtct---tttcgtgaactacattttttgaaatttttttggaagtaaatatttatactttgtgcagGTAGATGGCATGGATGCTCTTGCTGTGAAACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATT

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 2
---gtgcatcattaccttgttctta----ttaggtttcttgtaacctgcatcaagttagcaactttcttttgagtttgaccggttgctggtttgtatggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA
      || |  ||    | |   |    |||  ||| || |  |||||||       ||   |||  ||   ||||       |     ||| ||    |   ||||||||||| ||||||||  ||||||| ||||||||||| |||||||| ||| ||  ||| ||  |||| || || || 
ctgaaacacctatatacagctaagaaagcttaaattttttctttcctgcatt------gctgttttgattgttgtttttggaagtaaatatttatactt-tgtgcagGTAGATGGCATGGATGCTCTTGCTGTGAAACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATT

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 2
gtgcatcattaccttgttcttattaggtttcttgtaacctgcatcaagttagcaactttcttttg-agtttgaccggttgc-tggtttgtatggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA
 ||  |   | |||| |   |  |    ||| | |  | |     ||  ||  |  |||||||||  |  || |  ||| | || ||   ||      |||||||||||||||||||||  |||| || ||||| || |||| |||||||||| ||||||| ||  | || || || || 
-tggttaggtgccttttgtatgctttccttcatttg-cttattaaaaaatattatatttcttttgtggggtgtcttgttacatgtttcacatcttactacagGTAGATGGTATGGATGCTCTTGCGGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
----gtgcatcattaccttgttcttattaggtttcttgtaacctgcatcaagttagcaactttcttttgagtttgaccggttgctggtttgtatggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA
     |  |  | ||  |  || ||    || ||||| |||     || |  |||     | | |  || |||| |     ||    ||   ||       |||||||||||||||||||   ||||||| ||||| || |||| |||||||||| ||||||| ||  | || || || || 
tcttatcaaaaaataattaattttttgatgggttcttataaaaaatat-attttatttcttctgtggtgggttttattacatgt---ttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT

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|124925303|gb|EL003302.1|EL003302
EST:     CTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG                         GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTG
genomic: CTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAGgtcagctttt ... ggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTG
EST: gi|125286017|gb|EL300102.1|EL300102
EST:     TCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG                         GTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAG
genomic: TCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAGgtcagctttt ... ggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttagcaactttcttttgagtttgaccggttgctggtttgtatggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA
                     gtttgac  putative branch site (score: 4)
           tttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatcattaccttgttcttattaggtttcttgtaacctgcatcaagttagcaactttcttttgagtttgaccggttgctggtttgtatggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - cattacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttgt