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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagttatatccccccccccctctgttttttcctcttcattgcacatttctagtctgaacactggttaaattggtccattgttttgtgatttagGTTATGATATTCTTCAGTGCCCATGGTGTTCCGGTCAGCTACGTAGAGAATGCTGGAGATCCGTACCAGAAGCAGATGGAAGAGTGTATTGACTTGATAA

Basic information

species Arabidopsis thaliana
transcript AT5G26030.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G26030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g12560.2 (Oryza sativa), 3'ss of exon 6
-gtatagttatatccccccccccctctgttt----tttcctcttcattgcacatttctagtctga-acactggttaaattggtccattgttttgtgatttagGTTATGATATTCTTCAGTGCCCATGGTGTTCCGGTCAGCTACGTAGAGAATGCTGGAGATCCGTACCAGAAGCAGATGGAAGAGTGTATTGACTTGATAA
 ||| |  ||  ||   ||     | |        ||     || | |  | |     ||||||| | |||  | |   | |   |||  | |    ||||||||||||||||||||||||| ||||| || ||  | | ||| ||   | ||||||||||||| |||    | |||||||| || || ||||  ||||| |
cgtaaacgtaagtctgaccagaattatacaaaaagttggaaattgaatagatagaataagtctgatatactaatcatgattgcaaatt--tgtaatctttagGTTATGATATTCTTCAGTGCACATGGAGTACCACTTACCTATGTTACGGATGCTGGAGATCCTTACAGAGATCAGATGGAGGACTGCATTGCTTTGATCA

upper sequence: AT5G26030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G159013_T01 (Zea mays), 3'ss of exon 6
-------gtatagttatatccccccccccctctgttttttcctcttc-attgcacatttctagtctgaacactggttaaattggtccattgttttgtgatttagGTTATGATATTCTTCAGTGCCCATGGTGTTCCGGTCAGCTACGTAGAGAATGCTGGAGATCCGTACCAGAAGCAGATGGAAGAGTGTATTGACTTGATAA
       | |   | | |       |        |  |      |||   || |  ||  |  ||  || |||  ||| |||| |       |   |||   |||||||||||||||||||||| |||||||| ||  | | ||| || ||| ||||||||||||| |||    | |||||||| || |||||||  ||||| |
gctaaaagcagcatgacagttagttcatagataatcatgaaaaattctgctgtaatttcattctcataatact--ttatattgttgtgaaaatgaatgac--agGTTATGATATTCTTCAGTGCACATGGTGTGCCACTTACCTATGTTGAGGATGCTGGAGATCCTTACAGAGATCAGATGGAGGATTGTATTGCTTTGATCA

upper sequence: AT5G26030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G05390.1 (Glycine max), 3'ss of exon 6
----------------gtatagttatatccccccccccctctgttttttcctcttcattgcacattt----ctagtctgaacactggttaaattggtccattgttttgtgatttagGTTATGATATTCTTCAGTGCCCATGGTGTTCCGGTCAGCTACGTAGAGAATGCTGGAGATCCGTACCAGAAGCAGATGGAAGAGTGTATTGACTTGATAA
                | ||  ||  | |      |     |   ||     ||   |     ||||    | ||||||||     ||  |  | ||   || || | |   |||||| |||||||| ||||||||||| ||||| || ||||| ||||| ||| ||||||| ||||| ||||   | || ||||| ||||| ||   |||||| |
gtggattattcttgttgaatgctttcaacatggttcttacataaattgaaggctatgtgatgtattttactccagtctgaatcagagtgtatcttgt---ttattctatatattagGTAATGATATTTTTCAGTGCCCACGGTGTACCTGTCAGTTACGTTGAGGATGCTGGGGATCCATACCGAGACCAAATGGAGGAGTGCATCTTCTTGATCA

upper sequence: AT5G26030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G05320.1 (Glycine max), 3'ss of exon 6
-----gtatagttatatccccccccccctctgttttttcctcttcattgcacatttcta------gtctgaacactggttaaattggtccattgtttt----gtgatttagGTTATGATATTCTTCAGTGCCCATGGTGTTCCGGTCAGCTACGTAGAGAATGCTGGAGATCCGTACCAGAAGCAGATGGAAGAGTGTATTGACTTGATAA
      |||  || | |      |   |    |  ||    | | | |  |    | |        | | |   | |  | ||   ||   |||||||     |   |||||| |||||||| ||||||||||||||||| || ||||| ||||| ||| | ||||| ||||| ||||   | || ||||| ||||| ||   |||||| |
gtgggttattcttgtgttaaatgctttcaacatgattcgtacgtaaattgaaggctatgtgatgtattttactgcagtctgaaggtgtatcttgttttttctatatgttagGTAATGATATTTTTCAGTGCCCATGGTGTACCTGTCAGTTACGTTGAGGAAGCTGGGGATCCATACCGAGACCAAATGGAGGAGTGCATCTTCTTGATCA

upper sequence: AT5G26030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g00800.t01 (Vitis vinifera), 3'ss of exon 6
------------------gtatagttatatccccccccccctctgtttttt-----cctcttcattgcac-att--tctagtctgaacactg-gttaaattggtccattgttttgtga------tttagGTTATGATATTCTTCAGTGCCCATGGTGTTCCGGTCAGCTACGTAGAGAATGCTGGAGATCCGTACCAGAAGCAGATGGAAGAGTGTATTGACTTGATAA
                   | | ||| | |    ||       | || |||       | ||  |||||| |||  |  ||| | |   | |    ||||  || | |   ||| |        | ||||| ||||||||||||||||||||||| || || || || || || ||| ||||||||||||| |||    | |||||||| ||||| ||  |||| || |
gtgggttttgttcccgttatcttgttttctttttccataatattattctttgaaattttattatttgcaccattagttgagttttactgccgtaacaaatgagttcctaactttttagaggaattctagGTGATGATATTCTTCAGTGCCCATGGAGTACCCGTTAGTTATGTTGAGGATGCTGGAGATCCATACAGAGATCAGATGGAGGAGTGCATCTACTTAATCA

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|125100991|gb|EL156247.1|EL156247
EST:     TGGCTGACCTCATTGAGAAGGAGCTTCAAACTTTCTCTGATCCTAAGGAG                         GTTATGATATTCTTCGGTGCCCA
genomic: TGGCTGACCTCATTGAGAAGGAGCTTCAAACTTTCTCTGATCCTAAGGAGgtatagttat ... tgtgatttagGTTATGATATTCTTCAGTGCCCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcacatttctagtctgaacactggttaaattggtccattgttttgtgatttagGTTATGATATTCTTCAGTGCCCATGGTGTTCCGGTCAGCTACGTAGAGAATGCTGGAGATCCGTACCAGAAGCAGATGGAAGAGTGTATTGACTTGATAA
                                       ttgtttt  CT-rich tract
                          ttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagttatatccccccccccctctgttttttcctcttcattgcacatttctagtctgaacactggttaaattggtccattgttttgtgatttagGTTATGATATTCTTCAGTGCCCATGGTGTTCCGGTCAGCTACGTAGAGAATGCTGGAGATCCGTACCAGAAGCAGATGGAAGAGTGTATTGACTTGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA