Sequence
atgc intronic sequence ATGC exonic sequence...agatctcacgggtcacggcacatggctgattccaaaatggacagagtaaagagagagaatataaatgccattgatatgctgatgctttgttctcttgtagGTGCCCAAGCTTCTTGTCCATAGGATGTTTCCAAATGCTCGCTATTCTTTATGGATTGACGGAAAACTAGAACTTGTCGTCGATCCATATCAAATTCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G28240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 5
agatctcacgggtcacggcacatggctgattccaaaatggacagagt--------aaagagagagaatataaatgccattgatatgctgatgctttgttctcttgtagGTGCCCAAGCTTCTTGTCCATAGGATGTTTCCAAATGCTCGCTATTCTTTATGGATTGACGGAAAACTAGAACTTGTCGTCGATCCATATCAAATTCTTG
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----attgaaaataacaaaa-atatctcattcagaaactgttgtattttcttgctcataaagtagtactttaatgtaattgtaacgtaagttaccttttct---gcagATTCCTAAGCTTCTGTTGCATAGAATGGTTCCAAATGCCCGCTATTCTATATGGCTTGATGGAAAGCTTGAGCTTGTTGTTGATCCATATCAAATCCTTG
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G31680.1 (Glycine max), 3'ss of exon 5
agatctcacgggtcacggcacatggct-gattccaaaatggacagag---taaagagagagaatataaatgccattgatatgctgatgctttgttctcttgtagGTGCCCAAGCTTCTTGTCCATAGGATGTTTCCAAATGCTCGCTATTCTTTATGGATTGACGGAAAACTAGAACTTGTCGTCGATCCATATCAAATTCTTG
|| | | || || | | | | || | | || | | || || || | | || | | || | | | || | || |||||| | | ||||| || |||| ||||||||||||||| ||||| |||| || || || || ||||| || |||||||||||||||||||
gaattgaataaaattaaacttttgactaggtgctgatgtgttttcatgttcctaaagtagtactttacataccctataaattttaccaccttttccac----agATTCCAAAGCTTTTGTTGCATAGATTGGTTCCGAATGCTCGCTATTCTATATGGCTTGATGGGAAGCTTGAGCTTGTTGTGGATCCATATCAAATTCTTG
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G24770.1 (Glycine max), 3'ss of exon 5
agatctcacgggtcacggcacatggct-gattccaaaatggac---agagtaaagagagagaatataaatgccattgatatgctgatgctttgttctcttgtagGTGCCCAAGCTTCTTGTCCATAGGATGTTTCCAAATGCTCGCTATTCTTTATGGATTGACGGAAAACTAGAACTTGTCGTCGATCCATATCAAATTCTTG
|| | | || || | | | | || | || | | | || | | | | | | | || | | | || | || |||||||| | ||||| || |||| ||||||||||||||| ||||| |||| || || || || ||||| || |||||||||||||||||||
gaattgaataaaattaaacttttgcctaggtgctgatgtgttttctcattcctaaagtagtactttgcatactctgtaacttttactaccttttccac----agATTCCAAAGCTTCTGTTGCATAGATTGGTTCCGAATGCTCGCTATTCTATATGGCTTGATGGGAAGCTTGAGCTTGTTGTGGATCCATATCAAATTCTTG
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G31260.1 (Glycine max), 3'ss of exon 5
-----agatctcacgggtcacggcacatggctgattccaaaatggacagagtaaagagagagaatataaatgccattgatatgctgatgctttgttctcttgtagGTGCCCAAGCTTCTTGTCCATAGGATGTTTCCAAATGCTCGCTATTCTTTATGGATTGACGGAAAACTAGAACTTGTCGTCGATCCATATCAAATTCTTG
| || || | | | | | | || | | | | | || | | ||| ||| | || | ||| | || ||| | || | || |||||||| | ||||| ||| |||||||||| | ||||||| ||||| |||| ||||| || || ||||| || |||||||||||||| ||||
gtttaaaataacaaaaatatctcagtcagac--actgttgtattttcttgttcataaaatagtacttttatgtacttgtaa--cttaagctatcttttct-gcagATTCCAAAGCTTCTGTTGCATAGAATGGTTCCAAATGCCCACTATTCTATATGGCTTGATGGAAAGCTTGAGCTTGTTGTTGATCCATATCAAATCCTTG
upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 5
agatctcac---gggtcacggcacatggctgatt-ccaaaatggacagagtaaagagagagaatataaatgccattgatatgctgatgctttgttctcttgtagGTGCCCAAGCTTCTTGTCCATAGGATGTTTCCAAATGCTCGCTATTCTTTATGGATTGACGGAAAACTAGAACTTGTCGTCGATCCATATCAAATTCTTG
|| || | | | || | | || | | || | | || | | |||| || || || | ||| || || | | |||| || |||||||| | ||||||||||| || ||||||||||||||| | |||||||| ||||| || || ||||| || ||||||| |||||||||||
agttccagtttagagaaaaaatacttagttgctaacttgcattaatgtttcatcaaggtgtattttaaaccccctttg-atccaaatggtt---tccatggcagGTTCCAAAGCTTCTACTGCATAGGATGTTCCCTAATGCTCGCTATTCTCTGTGGATTGATGGAAAGCTTGAGCTTGTGGTGGATCCATTTCAAATTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaagagagagaatataaatgccattgatatgctgatgctttgttctcttgtagGTGCCCAAGCTTCTTGTCCATAGGATGTTTCCAAATGCTCGCTATTCTTTATGGATTGACGGAAAACTAGAACTTGTCGTCGATCCATATCAAATTCTTG
tgctgat putative branch site (score: 3)
tgctttgttctctt CT-rich tract
agaatataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatctcacgggtcacggcacatggctgattccaaaatggacagagtaaagagagagaatataaatgccattgatatgctgatgctttgttctcttgtagGTGCCCAAGCTTCTTGTCCATAGGATGTTTCCAAATGCTCGCTATTCTTTATGGATTGACGGAAAACTAGAACTTGTCGTCGATCCATATCAAATTCTTG
- - - - - - - - - - - - - - - -ccaaaat
- - - - - - - - - - - - - - - - - - - - - - - -aaagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc