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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttctattatttctgatgtacatgaaaagctctgaatccttaatttgcttctgtttctctgcctggtgttttgaaattacatgttgatatcccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC

Basic information

species Arabidopsis thaliana
transcript AT5G27640.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 8
gtatgtttctattatttctgatgtacatgaaaagctctgaatccttaatttgcttct-----gtttctctgcctggtgttttgaaattacatgttgatatcccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
                      |||  || ||   ||||  | ||| ||    ||       ||| |     ||  || |    | | | || |  |  |    |    ||||   ||| || ||||| ||  |||| | ||||||| ||||||| || || |||||||| || || |||||||||||||||||||  |||||||| ||||
----------------------gtaagtgcaattttctg--tgcttcatcccttttgaggaagttccgtcaactaatggtgaagactaaaatctataatttttattgaaagGTGAGCCTTGTGCAAATTCCTGGCAAAGAGGAGCTGCGGCAGAAAAACCTTTTCAGTGTCAGTGATTGCAAGATGTACTGGCAGAACAGTGGAGAATATC

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
gtatgt-ttctattatttctgatgtacatga---aaagctctgaat--ccttaatttgcttctgtttctctgcctggtgttttgaaattac-atgttgatatccctt-------cttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
||| || |  | || | | | |||||  ||    |||| | ||  |  | |   | |  |  ||  |       |  | |||   |||||  || |  || | | ||        |  |||||   ||  | |||||||| ||||| ||||| || |||||||| || || |||||||| || |||||||||||||||||||| || | |||||| || |
gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 11
gtatgtttctattatttctgatgtacatgaaaagct-ctgaatccttaatttgctt--ctgtttctctgcctggt--------gttttgaaattac---atgttgatatccctt-------cttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
||| || | |||| |||||    | |||| |   ||  ||||   ||| ||| |||   | ||    ||  ||||         |||   |||||    || || || | | ||        |  |||||   ||  | |||||||| ||||| | ||| || ||||||||||| || ||||||||  | |||||||||||||||||||| || | |||||| || |
gtaagtatgtattttttct----ttcatgtaggtctattgaagttttattttacttggttattgtaatgaatggtcatatattatttattaattattttatatttatgttctttgacatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCGGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
gtatgtttctattatt-tctgatgtacatga---aaagctctgaat--ccttaatttgcttctgtttctctgcctggtgttttgaaattac---atgttgatatccctt-------cttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
||| |||| | || || | | |||||||||    |||| | ||  |  | |   | |  |  ||  |       |  | |||   |||||    || |  || | | ||        |  |||||   ||  | |||||||| ||||| | ||| || ||||||||||| || |||||||| || ||||||||||| |||||||| || | |||||| || |
gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatatatttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 8
-----------------gtatgtttcta-ttatttctgatgtacatgaaaagctctgaatccttaatttgcttctgtttctctgcctggtgttttgaaattacat--gttgatatcccttctt--------cagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
                  |      | | || | |||  | |  ||     |||     ||||| | |   ||   | |||      |     || |||||  ||   | |   |  |||| |        |||||    || || |||||||| || || | |||| ||||||||||||||||||| ||||| || |||||||| ||||||||||| || | ||| || || |
gtgagtgcagctgttccatgcaaaaccagttttctcttctttttatattttgcttctcttcctttaatattttgcttctcttccatagacaagttaaaatttgattaatggtctttacttcataaaatatgcagGTGAGTCTGGTTCAAATCCCCAGTAAAGAGGAGTTGAGGCAGAAGAATCTCTTTAGTGTTAGTGACTGCAAAATGTACTGGCAAAGCAATGGGGACTACC

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ13839 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtttctattatttctgatgtacatgaaaagctctgaatccttaatttgcttctgtttctctgcctggtgttttgaaattacatgttgatatcccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
                                         |   || ||   ||   ||||||| | || ||   ||   ||   | ||||     ||||  ||||||  ||| || ||||| ||  ||| ||  || |||||||||||||| || |||||||| || |||||||||||||||||||| || |  ||||| ||||
----------------------------------------gtatgtatttgtgtttgatttctctacatg-tgacctg--gtttgctcttga-----cttcaacagGTTAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC

upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ12681 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtttctattatttctgatgtacatgaaaagctctgaatccttaatttgcttctgtttctctgcctggtgttttgaaattacatgttgatatcccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
                                         |   || ||   ||   ||||||| | ||      |||  |    || |   | |  |||  |||||   ||| || ||||| ||  ||| ||  || |||||||||||||| || |||||||| || |||||||||||||||||||| || |  ||||| ||||
----------------------------------------gtatgtatttgtgtttgatttctctacatg------tgacctggtttgctctcaac--ttcaacagGTCAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC

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|125318345|gb|EL332430.1|EL332430
EST:     TCCTTTCATTGTTTGTTCCTGAACAAGGTGGTGGAAACCAACCTGCGAAG                         GTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAA
genomic: TCCTTTCATTGTTTGTTCCTGAACAAGGTGGTGGAAACCAACCTGCGAAGgtatgtttct ... ccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAA
EST: gi|47832098|gb|CK121782.1|CK121782
EST:     TCCTTTCATTGTTTGTTCCTGAACAAGGTGGTGGAAACCAACCTGCGAAG                         GTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTC
genomic: TCCTTTCATTGTTTGTTCCTGAACAAGGTGGTGGAAACCAACCTGCGAAGgtatgtttct ... ccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTC
EST: gi|164100692|gb|ES136495.1|ES136495
EST:     GAACAAGGTGGTGGAAACCAACCTGCGAAG                         GTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTC
genomic: GAACAAGGTGGTGGAAACCAACCTGCGAAGgtatgtttct ... ccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttctgtttctctgcctggtgttttgaaattacatgttgatatcccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
                                   tgttgat  putative branch site (score: 4)
                                         tatcccttcttc  CT-rich tract
                      ttttgaaattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttctattatttctgatgtacatgaaaagctctgaatccttaatttgcttctgtttctctgcctggtgttttgaaattacatgttgatatcccttcttcagGTTGCCCTAGTCCAAATCCCGAGCAAGGTGGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA