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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaagttcattggcattgtttctgtcaagattttctcagctgctaagatatagctagtttacatctatcgtttctgaaaactaagactcttgttctcagATTTCTCTGTCCTCCGTAACATCTATAGTGGATGGCCTGAAGAGGTTGTACATTCAGAAGCTGAAGCCACTTGAAGTAGCATATCGGTTTAACGATTTTG

Basic information

species Arabidopsis thaliana
transcript AT3G20290.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 7
--acaaagttcattggcattgtttctgtcaagattttctcagctgctaagata-tagctagtttacatctatcgtttctgaaaactaagactcttgttctcagATTTCTCTGTCCTCCGTAACATCTATAGTGGATGGCCTGAAGAGGTTGTACATTCAGAAGCTGAAGCCACTTGAAGTAGCATATCGGTTTAACGATTTTG
   |  |  |   |    |  |||||    || ||| ||  ||   |    || |  ||||  |  ||| ||  ||||     | |        ||| ||||| |  |||| || ||||| ||||| ||| | |||||| ||||||||||||||||||||||||| |||||| | || ||  ||||||| |||||||||||||
tgtcttaacttgctctt-tcatttctaatgag-tttcctatgcacttcttctagtttctagcctg-atccattctttccctgtatttctttgtatgtgctcagGTACCTCTATCTTCCGTTACATCAATAATTGATGGCTTGAAGAGGTTGTACATTCAGAAGCTCAAGCCATTAGAGGTTACATATCGTTTTAACGATTTTG
















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|116430168|gb|EG472760.1|EG472760
EST:     CAGACACCTCACTTACAGCTCACTGGTTCTCTTCAAAATCTTCAAAAAAG                         ATTTCTCTGTCCTCCGTAACATCTATAGTGGATGGCCTGAAGAGGTTGTAC
genomic: CAGACACCTCACTTACAGCTCACTGGTTCTCTTCAAAATCTTCAAAAAAGgtttgttttg ... ttgttctcagATTTCTCTGTCCTCCGTAACATCTATAGTGGATGGCCTGAAGAGGTTGTAC
EST: gi|124952792|gb|EL028035.1|EL028035
EST:     CAGACACCTCACTTACAGCTCACTGGTTCTCTTCAAAATCTTCAAAAAAG                         AATTTCTCTGTCCTCCGTAACATCTA
genomic: CAGACACCTCACTTACAGCTCACTGGTTCTCTTCAAAATCTTCAAAAAAGgtttgttttg ... ttgttctcagA-TTTCTCTGTCCTCCGTAACATCTA
EST: gi|124811087|gb|EH895953.1|EH895953
EST:     CAGACACCTCACTTACAGCTCACTGGTTCTCTTCAAAATCTTCAAAAAAG                         ATTTCTCTGTCCTCCGTAACAAATCTATAGTGGATGGCCTGAAGAGGTT
genomic: CAGACACCTCACTTACAGCTCACTGGTTCTCTTCAAAATCTTCAAAAAAGgtttgttttg ... ttgttctcagATTTCTCTGTCCTCCGTAACA--TCTATAGTGGATGGCCTGAAGAGGTT
EST: gi|124814425|gb|EH899291.1|EH899291
EST:     CTCTTCAAAATCTTCAAAAAAG                         ATTTCTCTGTCCTCCGTAACATCTATAGTGGATGGCCTGAAGAGGTTGTAC
genomic: CTCTTCAAAATCTTCAAAAAAGgtttgttttg ... ttgttctcagATTTCTCTGTCCTCCGTAACATCTATAGTGGATGGCCTGAAGAGGTTGTAC
EST: gi|125242343|gb|EL256428.1|EL256428
EST:     CAGACACCTCACTTACAGCTCACTGGTTCTCTTCAAAATCTTCAAAAAAG                         ATTTCTCTGTCCTCCGTAACATCTATAGTGGAT
genomic: CAGACACCTCACTTACAGCTCACTGGTTCTCTTCAAAATCTTCAAAAAAGgtttgttttg ... ttgttctcagATTTCTCTGTCCTCCGTAACATCTATAGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatatagctagtttacatctatcgtttctgaaaactaagactcttgttctcagATTTCTCTGTCCTCCGTAACATCTATAGTGGATGGCCTGAAGAGGTTGTACATTCAGAAGCTGAAGCCACTTGAAGTAGCATATCGGTTTAACGATTTTG
                                          ctcttgttctc  CT-rich tract
                                aaaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaagttcattggcattgtttctgtcaagattttctcagctgctaagatatagctagtttacatctatcgtttctgaaaactaagactcttgttctcagATTTCTCTGTCCTCCGTAACATCTATAGTGGATGGCCTGAAGAGGTTGTACATTCAGAAGCTGAAGCCACTTGAAGTAGCATATCGGTTTAACGATTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
acaaagt
- - - - - - - - - - - - - - - - -ttctcag
- - - - - - - - - - - - - - - - - - - - ctgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa