Sequence
atgc intronic sequence ATGC exonic sequencegttcttgacttaaaacaatcttattgttcatgtcaattgttatttctcaaaactaatctcattgtaatgcttttaccagGGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20650.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G22390.1 (Glycine max), 3'ss of exon 3
--gttcttgacttaaaacaatct-tattgttcatgtcaattgttatttctcaa--aactaatctcattgt--aatgcttttaccagGGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCG
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gtcttcatggttttcagttgtttatataccaaaagtcattcccagtttcttggctaatcatccttttttttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACAAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCA
upper sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G41190.1 (Glycine max), 3'ss of exon 3
--gttcttgacttaaaacaatc--ttattgttcat--gtcaattgttatttctcaa--aactaatc----tcattgtaatgcttttaccagGGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCG
||| || || | | |||| || | || | ||||| ||| | | | || | ||||||||||||||||| | ||||| ||||| ||||| | ||| || || |||||||| ||||| ||||||||||| |||
gtgttaatggttttcatttgttgtttatataccaaaagacattctcagtttcttggctaaccatccttttttgtttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACAAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCG
upper sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G17220.1 (Glycine max), 3'ss of exon 4
----------------------gttcttgacttaaa--acaatcttattgttcatgtcaattgttatttctcaaaactaatctcattgtaatgcttttaccagGGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCG----
||| | ||| ||| ||| | | | | || | || | | | | || | ||||||||||||||||| | ||||| ||||| |||| | ||| || || |||||||| ||||| ||||||||||| |||
gtgttaatggttttcagttgttgtttatataccaaaagacattctcagtttcttggctaaccatagagtcc---atccttttttgtttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT
upper sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 3
--gttcttga---cttaaaacaatcttattgttcatgtcaattgttatttctcaaaactaatc-----tcattgtaatgcttttaccagGGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCG
||| | || ||| | | ||| |||| || || || || | | || | | | || | | ||| || ||||||||||| | ||||| ||||| ||||| | || || ||||||||||| || |||||||||||||| |||
gtgttatagagcttttatatctatcaaattga--gtggcagttcttttatgctaatattctttcttgttcttcacccttttttcactagGGTGGTGATCTAATCAAATGGGACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGMapped 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|19875466|gb|AU236297.1|AU236297EST: AGCTTTATGCTCGTNCTGACGATGCTGTTCTCGACCTTGCCTGTGGGAAG GGTGGTGATTTGATCAAGTGGGAT
genomic: AGCTTTATGCTCGTCCTGACGATGCTGTTCTCGACCTTGCCTGTGGGAAGgttcttgact ... cttttaccagGGTGGTGATTTGATCAAGTGGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcatgtcaattgttatttctcaaaactaatctcattgtaatgcttttaccagGGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCG
aactaat putative branch site (score: 2)
cttttacc putative PPT
aattgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttgacttaaaacaatcttattgttcatgtcaattgttatttctcaaaactaatctcattgtaatgcttttaccagGGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG