Sequence
atgc intronic sequence ATGC exonic sequence...ggcatgaggtgtttaatagtctgagcttgttagccatactccattgtactactctagacttatgtatcgagactctggcttaacacatgaggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G21720.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G10130.1 (Glycine max), 3'ss of exon 4
ggcatgaggtgtttaatagtctgagcttgttagccata-ctccattgtactactctagacttatgtatcgagac---------tctggcttaacacatgaggatt-ttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT
||||| || || || ||| ||| | || | | | || | |||| || || | |||||| ||| | |||||| | ||||||||||| ||||| || || |||||||| || |||||||| || ||||||||| ||||||| |||||||| ||||| || ||||
---------gatttaact-tcgaagatttttaattatagtttcacaatgtt-cattaaagatatgcatgcagcttatattttttttggcttggtttctgatcttgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT
upper sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G24270.3 (Glycine max), 3'ss of exon 4
---ggcatgaggtgtttaatag-tctgagc-ttgttagccatactccattgtactactctagacttatgtatcgagactctggcttaacacatgaggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT
| || || || | | | ||| | ||| || | |||| | || ||||| | | |||| || | || | || |||||| | ||||||||||| ||||| || || |||||||| || |||||||| || ||||||||| ||||||| |||||||| ||||| || ||
cttgtgatttaacgtcaaagatctttaagcatagtttctcaatgttcattaaagagacacag-cttatattttttctgcctggttt--ctaatcatgaca--cagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTT--
upper sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 3
--------ggcatga--ggtgtttaatagtctgagcttgttagccatactccattgtactactctagacttatgtatcgagactctggcttaacacatgaggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT
| ||| | | ||||| | || || || || || ||| | | |||||| || | | ||| || | || | ||||||| | || ||||||||||||||||| || |||||||| || |||||||| || ||||||||| | ||||| ||||| || |||||||| ||||
attcttgaaacttgatagatatttaa-aatccagtttttttcatgat-cttcatagagaag----aaacttattcat-gttcccttggtttcttaactgtga---ctcagGAACCAGAAGAATTGTTCGAGACAATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTAAGTGGCTGGGGTGGACATGTTTATGTTGT
upper sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G24270.1 (Glycine max), 3'ss of exon 4
---ggcatgaggtgtttaatag-tctgagc-ttgttagccatactccattgtactactctagacttatgtatcgagactctggcttaacacatgaggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT
| || || || | | | ||| | ||| || | |||| | || ||||| | | |||| || | || | || |||||| | ||||||||||| ||||| || || |||||||| || |||||||| || ||||||||| ||||||| |||||||| ||||| || ||||
cttgtgatttaacgtcaaagatctttaagcatagtttctcaatgttcattaaagagacacag-cttatattttttctgcctggttt--ctaatcatgaca--cagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT
upper sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 5
ggcatgaggtgtttaatagtctgagcttgttagccatactccattgtactactctagacttatgtatcgag--actctggcttaacacatgag--gattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT
|| | | | || || | |||| ||| | | || | | | || ||| || | || || | | | | |||||||| |||||||||| || |||| || || |||||||| |||||||| || || ||||| || |||||||||||||||| ||||| || ||||
--attgtgctaagatacagcatgctccctttagtcatctttcgttc--ccatgtcaagctaatgggatcagctgcattgactctttattttaactattattcagGAACCTGAGGAATTATTTGAGATCATCTCTCAAGCACTGCTCTCATCAGTAGATCGTGACTGCTTGAGTGGTTGGGGAGGACATGTCTATGTTGTMapped 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|86076686|gb|DR372443.1|DR372443EST: CTTCAGAATCACTCTATGGAGCTTGTGAGGCAATGTACAAGCCAGATATG GAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTT
genomic: CTTCAGAATCACTCTATGGAGCTTGTGAGGCAATGTACAAGCCAGATATGgtttgcccgc ... ggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTT
EST:
gi|124811214|gb|EH896080.1|EH896080EST: CAAGCCAGATATG GAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCAT
genomic: CAAGCCAGATATGgtttgcccgc ... ggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCAT
EST:
gi|124777885|gb|EH867828.1|EH867828EST: CTTCAGAATCACTCTATGGAGCTTGTGAGGCAATGTACAAGCCAGATATG GAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCA
genomic: CTTCAGAATCACTCTATGGAGCTTGTGAGGCAATGTACAAGCCAGATATGgtttgcccgc ... ggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtactactctagacttatgtatcgagactctggcttaacacatgaggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT
gcttaac putative branch site (score: 3)
ttttc putative PPT
ttatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcatgaggtgtttaatagtctgagcttgttagccatactccattgtactactctagacttatgtatcgagactctggcttaacacatgaggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT
- - - - - - - - - - - - - - - - -ccatact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaca