Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatctttgaaacttccctgtctgatactgtgaggaaaatagtgtgagattgacatgagtttcacttcttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51880.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G28820.1 (Glycine max), 3'ss of exon 5
---------------gtaagtatctttgaaacttccctgtctgatactgtgaggaaaatagtgtgagattgacatgagtttcacttcttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
|| ||| | ||| || | || ||| | | | | ||| | | | | || || ||||||||| |||||||||||||||| || |||||||||||||||||||| ||||| || | || | || || | ||||| |
gaattcagtatatctatatatatgtaccaaatgaacccattctattgaagaagggattaattttttaattaattttgactcctctctttgaaatgtaaagGAGAAAGCTCCATATGAAGCCAAGGCTGCAAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG
upper sequence: AT3G51880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G28820.4 (Glycine max), 3'ss of exon 5
------------gtaagtatctttgaaacttccctgtctgatactgtgaggaaaatagtgtgagattgacatgagtttcacttcttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
|| ||| | ||| || | || ||| | | | | ||| | | | | || || ||||||||| |||||||||||||||| || |||||||||||||||||||| ||||| || | || | || || | ||||| |
ttcagtatatctatatatatgtaccaaatgaacccattctattgaagaagggattaattttttaattaattttgactcctctctttgaaatgtaaaggagAAAGCTCCATATGAAGCCAAGGCTGCAAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGAGAAAAAGCAG
upper sequence: AT3G51880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G08270.1 (Glycine max), 3'ss of exon 5
---------------gtaagtatctttgaaacttccctgtctgatactgtgaggaaaatagtgtgagattgacatgagtttcacttcttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
|| ||| | ||| | | || ||| | || | | ||| | | || | || || ||| ||||| |||||||||||||||| || ||||| |||||||||||||| ||||| || | || | || || | ||||| |
attccagtaatatcaatatatatgtaccaaatgaactcattctattgaagaagggatttatttttttattaatttttattcctctcattgaaatgtgaagGAGAAAGCTCCATATGAAGCCAAGGCTGCGAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG
upper sequence: AT3G51880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G08270.5 (Glycine max), 3'ss of exon 4
gtaagtatctttgaaacttccctgtctgatactgtgaggaaaatagtgtgagattgacatgagtttcacttcttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
||| | ||| | | || ||| | || | | ||| | | || | || || ||| ||||| |||||||||||||||| || ||||| |||||||||||||| ||||| || | || | || || | ||||| |
----atatgtaccaaatgaactcattctattgaagaagggatttatttttttattaatttttattcctctcattgaaatgtgaaggagaaagctccatatgaagCCAAGGCTGCGAAAAGGAAAGCTGAGTATGAAAAACTTATCAAAGCTTATGATAAAAAGCAG
upper sequence: AT3G51880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0067g00640.t01 (Vitis vinifera), 3'ss of exon 5
----gtaagtatctttg------aaacttccctgtctgatactgtga---ggaaaatagtgtgag--attgacatgagtttcacttcttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
|||||| || || | | |||| | || | | ||| |||||| ||| | | || | || | |||| |||||||||||||||| ||||| |||||||||||| | || ||||| |||| |||| ||||||||||| || |
gtctgtaagttctcttctccatcaagagtttcaatctggcttggagactggtgatgcttcatgaactattgacctgattcttctttactgggttttccagGATAAAGCTCCATATGAAGCTAAAGCAGCAAAAAGGAAATCGGACTATGAAAAGCTTATGGCAGCATACAACAAGAAACAG
upper sequence: AT3G51880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g02200.t01 (Vitis vinifera), 3'ss of exon 5
----------gtaagt----atctttgaaacttccctgtctgatactgtgaggaaaatagtgtgagattgacatgagtttcactt--cttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
||||| || | | || | || | | || | | | ||| | |||| ||| ||| | | |||| |||||||||||||||||||| | ||||||||||||| ||| ||||| || || || ||| |||| |||||||| || |
tgtaagatcagtaagctttcatatataaattgactctcataaaaaatggcattgattcactgtattactgacctgaaaaattcttgacctggtttg-gaagGAAAAAGCTCCATATGAGGCCAAAGCTGCAAAAAAGAAGGCTGAGTACGAAAAAATTATGAATGCTTACAACAAGAAGCAGMapped 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|163993175|gb|ES163743.1|ES163743EST: CTGCTGTTGGGAAAGCTGGAGGGCAGAAATGGAAGGCAATGTCTCAAGCT GAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGC
genomic: CTGCTGTTGGGAAAGCTGGAGGGCAGAAATGGAAGTCAATGTCTCAAGCTgtaagtatct ... ctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtgaggaaaatagtgtgagattgacatgagtttcacttcttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
gattgac putative branch site (score: 3)
tttcacttcttccttt putative PPT
aaaatagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatctttgaaacttccctgtctgatactgtgaggaaaatagtgtgagattgacatgagtttcacttcttcctttgtaaagGAAAAAGCTCCATATGAAGAGAAAGCTGCAAAAAGGAAAGCTGAATATGAGAAGCAAATGGATGCATACAACAAAAACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA