Sequence
atgc intronic sequence ATGC exonic sequence...actgctaaaattatgactcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79650.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 1
actgctaaaattatgactcgcgaatccaatc-tggtt-tggtcaagttgattatgttagtcttcaaa---tcattaaatctgggcatgatgtgc-ttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
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------ataatgcttgtcagctaactgttttgtgatcgtagttgaatgagttttattggcattcaatattttgtcaaggttctactaaaggttccttatttaccagATTATGGCTGTGAAGAAGAATATAGAAGAGATACAAGGGAAAGACAGCTATCCATGGGGCCAACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATG
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G23930.2 (Glycine max), 3'ss of exon 1
-actgctaaaattatgactcgcgaa-tccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
| | | || | | | ||| || | | | | | | | | | || | || || | | || | || | | | | || | ||||| || ||||||||||| |||||| |||||||||||| ||||| |||||||| ||||||||||||||||||||||| || |||||||||||||
taattttgaagtgctattttttgaaatctattgtttatcagctgaaattgtcaatttgttgtttaattagctgaagttt--tctgcttttttgtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
----actgctaaaattatgactcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtt-tttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
| | | || | | | | ||| | || |||| || || | | | | | | |||| | | | | | | |||| | || | ||||| || ||||||||||| |||||| |||||||||||| ||||| |||||||| ||||||||| ||||||||||||| || |||||||||||||
ggaaaattttgaagtgctatgtttcaaattctatt--gtttatc--agccgaaattatcaatttgttgtttattagctgagtgt-tcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G44910.1 (Glycine max), 3'ss of exon 1
actgctaaaattatgac-tcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
| | || || | | | || ||||| | || | || || ||| | | | || | | ||| | | | | |||| ||||| || ||||||||||| |||||| |||||| ||||||||||| |||||||| ||||||||| | ||||||||||| || |||||||||||||
gtcagtcatatgatctcattcccaacccaattctgcttt-ttaatttcattcttccaaatcctatgcatttcttaattgtgatgttttatcttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G44910.2 (Glycine max), 3'ss of exon 1
actgctaaaattatgac-tcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
| | || || | | | || ||||| | || | || || ||| | | | || | | ||| | | | | |||| ||||| || ||||||||||| |||||| |||||| ||||||||||| |||||||| ||||||||| | ||||||||||
gtcagtcatatgatctcattcccaacccaattctgcttt-ttaatttcattcttccaaatcctatgcatttcttaattgtgatgttttatcttcacctcagATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATG------------------
upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 1
--actgctaaaattatgactcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
||| | | | | | ||| || || || |||| | | | | || ||| || || || || ||| | |||||||| ||||| || || |||||| ||||||||||||||| ||||| |||||||| ||||| |||||||| |||||||| || ||||||||||
actctgttcatctgtgttcccatgaaatatatttg-cctgagtgtgttgcaaacaccacatgacttaatgaaaaccttggtaattgcttgtttaattg-aagGTTATGGCGGTAAAGAAAAACATTGAAGATGTACAAGGAAAAGACAACTATCCGTGTGGGCAACAATTATTGATTCATAATGGAAAGGTCTTGAAAGATGMapped 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|163991191|gb|ES154720.1|ES154720EST: TTTGAAATTAGGGTTTTACCCTCCGATACG ATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTAT
genomic: TTTGAAATTAGGGTTTTACCCTCCGATACGgttagttcta ... tgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
agttgat putative branch site (score: 5)
cttgttttt putative PPT
ttcaaatcattaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgctaaaattatgactcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG