Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgagtctaaattttgttgtagtgttgtctattggtagtattaaaatagtaacaaatcatgcgaattttcttttatcacggaatgcagGTTGCAGATTTTGGTTCATTGGAGCTCTCCCCAGTCGATGGCCGGACTCTAACTGATTTTATGCACACAAGAGGTCTTCGGATGCGTTCTTTAGGATATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01320.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 13
gtaa--atgagtctaaattttgttgtagtgttgtctattggtagtattaaaatagtaacaaatcatgcgaatttt--cttttatcacggaatgcagGTTGCAGATTTTGGTTCATTGGAGCTCTCCCCAGTCGATGGCCGGACTCTAACTGATTTTATGCACACAAGAGGTCTTCGGATGCGTTCTTTAGGATATG
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gtaaggatggaattttatttggttg-attgtttgcaaggcttttggttaatatgacttttg-tgatctttattatagtcttaattgtggaatacagGTAGCCGATTTTGGCTCATTGGAACTCTCACCAGTTGATGGACGCACTCTAACTGATTTTATGCATACTCGGGGTCTACGAATGCATTCTCTTGGACATG
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 11
gtaaatgagtctaaattttgttgtagtgttgtctattg-gtagtattaaaatagtaacaaatcatgcgaattttctttta-------tcacggaatgcagGTTGCAGATTTTGGTTCATTGGAGCTCTCCCCAGTCGATGGCCGGACTCTAACTGATTTTATGCACACAAGAGGTCTTCGGATGCGTTCTTTAGGATATG
| || || | ||| || | || | | |||| | || || || | || | || ||| || || | ||||| ||||| || ||||| || |||||||| ||||| ||||| ||||| || |||||||||||||||||||| || | ||||| || ||||||||| | ||| |||
----gtaaggatagaatttatt-tggt-tgattgattgcacggcttttggttaata-tgactctggtgatctttattgtagtcttaattgtggaatacagGTAGCCGATTTCGGCTCATTGGAACTCTCACCAGTTGATGGACGCACTCTAACTGATTTTATGCATACTCGGGGTCTACGAATGCGTTCTCTTGGACATG
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 13
gtaa--atgagtctaaattttgttgtagt--gttgtctattggtagtattaaaatagtaacaaatcatgcgaattttcttttatcacgg------aatgcagGTTGCAGATTTTGGTTCATTGGAGCTCTCCCCAGTCGATGGCCGGACTCTAACTGATTTTATGCACACAAGAGGTCTTCGGATGCGTTCTTTAGGATATG
|||| | | || | ||| | | || | | | | | ||| | || | | || | | | || | ||| |||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||| ||||| || ||||||||||| ||||||||| | ||| |||
gtaaccactgaataatatctgattgaacttgattatgtctgcatgaaaataaggttgtggtgatttctgtttctgtgtctgcatgaaaattgtccaattcagGTTGCAGATTTTGGTTCATTGGAACTCTCACCAGTGGATGGTCGGACGCTGACCGATTTCATGCATACTAGAGGTCTTCGAATGCGTTCTCTGGGACATG
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0002g01140.t01 (Vitis vinifera), 3'ss of exon 4
gtaa--atgagtctaaattttgttgtagt--gttgtctattggtagtattaaaatagtaacaaatcatgcgaattttcttttatcacgg------aatgcagGTTGCAGATTTTGGTTCATTGGAGCTCTCCCCAGTCGATGGCCGGACTCTAACTGATTTTATGCACACAAGAGGTCTTCGGATGCGTTCTTTAGGATATG
|||| | | || | ||| | | || | | | | | ||| | || | | || | | | || | ||| ||||||||||||||||||||||||| ||||| ||||| ||||| | ||| || | ||||| ||||| || ||||||||||| ||||||||| | ||| |||
gtaaccactgaataatatctgattgaacttgattatgtctgcatgaaaataaggttgtggtgatttctgtttctgtgtctgcatgaaaattgtccaatttagGTTGCAGATTTTGGTTCATTGGAACTCTCACCAGTGGATGGTCAGACGCTGATCGATTTCATGCATACTAGAGGTCTTCGAATGCGTTCTCTGGGACATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtagtattaaaatagtaacaaatcatgcgaattttcttttatcacggaatgcagGTTGCAGATTTTGGTTCATTGGAGCTCTCCCCAGTCGATGGCCGGACTCTAACTGATTTTATGCACACAAGAGGTCTTCGGATGCGTTCTTTAGGATATG
tagtaac putative branch site (score: 1)
ttttcttttatcac putative PPT
tattaaaatagtaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgagtctaaattttgttgtagtgttgtctattggtagtattaaaatagtaacaaatcatgcgaattttcttttatcacggaatgcagGTTGCAGATTTTGGTTCATTGGAGCTCTCCCCAGTCGATGGCCGGACTCTAACTGATTTTATGCACACAAGAGGTCTTCGGATGCGTTCTTTAGGATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG