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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatggaaactgctttcagctacatttgtgcttgattttggctgcttaattgcttagcttcaaaagatcatgccatctaaaagatgtgtcctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG

Basic information

species Arabidopsis thaliana
transcript AT3G42050.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G06710.1 (Glycine max), 3'ss of exon 5
ttgatggaaactgctttcagctacatttgtgcttgattttggctgcttaattgcttagcttcaaaagatc---atgccatctaaaagatgtgtcc-tctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG
   |||||  |  |  | | | || |   |   |  |     ||   || |  || |   | |  | ||    |    | |||| |    | ||| |||||||| ||||| ||||| |||||||||||||| ||||| ||||| |||||||||||||| |   |  | ||
--aatgga--ccaccatgaaccacttagttaactagtccaccctagatactgtctcaaagttatgatatacaaaaaataactaacaatattatccatctttcagATTGCTCTGGAAAGGAAATTGGTTCATACAAGAGAAAAGTTGTAAGATCCTTGCTTTAGTTGTTAG

upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G25740.1 (Glycine max), 3'ss of exon 5
-ttgatggaaactgctttcagcta--catttgtgcttgattttggctgcttaattgcttagcttcaaaagatcatgccatctaaaagatgtgtcctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG
 | |||    ||   | |  | ||  |||||   ||   || |   | ||| |  | |  | |  | || |  |  | | |   || || |  | |||||||| ||||| ||||| |||||||||||||| ||||| ||||| ||||||||||| || |  ||  | ||
ctagataatgacatatgtttgttatgcattttgactattttctttgtacttcaaagttatgatatacaaaaaaaaactaac---aatattttccatctttcagATTGCTCTGGAAAGGAAATTGGTTCATACAAGAGAAAAGTTGTAAGATCCTCGCTTTAATTGTTAG

upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv16s0039g01610.t01 (Vitis vinifera), 3'ss of exon 5
------------------ttgatggaaactgctttcagctacatttgtgcttgattttggctgcttaattgctta-gcttcaaaagatcatgccatctaaaaga--tgtgtcct-----ctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG
                  || ||   || ||       ||| |  ||  ||||| |    |   |||||| |||| | | |  ||  | |||  | |||| |||  |||| | |     ||||||| ||||||||||| || ||||||||| | ||||| || ||||||||||| || ||   |||| | ||
gtagattacagcattttcttcatttgaattgtgaatgacta-aggtgcccttgactggatcaagttaatttcttatgttcctcaacttaatgaaaactaagagaattgtgactttgttactttcagATTGCTTTGGAAAGGTAATTGGTTCGTACAAGAGAAGAGCTGTAAGATTCTGGCTCTGATAGTGAG

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|47832017|gb|CK121701.1|CK121701
EST:     TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGCAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAACATCCT
genomic: TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
EST: gi|125189705|gb|EL204659.1|EL204659
EST:     TGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
genomic: TGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
EST: gi|86031310|gb|DR327063.1|DR327063
EST:     TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGGAAAAGGAAATTGGTTCATTCA
genomic: TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAG-GGAAATTGGTTCATTCA
EST: gi|116433606|gb|EG476198.1|EG476198
EST:     TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
genomic: TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
EST: gi|116433595|gb|EG476187.1|EG476187
EST:     TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
genomic: TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
EST: gi|86031307|gb|DR327060.1|DR327060
EST:     TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGGAAAGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
genomic: TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
EST: gi|86031303|gb|DR327056.1|DR327056
EST:     TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGGAAAGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
genomic: TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
EST: gi|86031311|gb|DR327064.1|DR327064
EST:     TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGGAAAGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
genomic: TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
EST: gi|86031304|gb|DR327057.1|DR327057
EST:     TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAG                         GTTGCTTTGGAAAGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT
genomic: TTCCATGATGAATCTTTGGCAAATGAGGATACTTATGAGCCTTTCTTGAGgtgagtccct ... cctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattgcttagcttcaaaagatcatgccatctaaaagatgtgtcctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG
                              atctaaa  putative branch site (score: 3)
                                          tgtcctctttc  putative PPT
                              atctaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatggaaactgctttcagctacatttgtgcttgattttggctgcttaattgcttagcttcaaaagatcatgccatctaaaagatgtgtcctctttcagGTTGCTTTGGAAGGGAAATTGGTTCATTCAAGAAAAAAGCTGTAAGATCCTTGCCTGGATAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - ctgcttt
- - - - - - - - - - - - - - - - - gattttg
- - - - - - - - - - - - - - - - - - - - - ctgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atctaaa