Sequence
atgc intronic sequence ATGC exonic sequence...gttttttaagcattaaggatgagatcaacacgaaactacttagtttagtagttacagtttctgatacaaattgtcttcatcgtgtttattttttatgcagGTTTTCTTGACAAAACATTACCGGAACAGAAGGACAAACGATCCAGAATTTGTGCTAGATCTTGAAGAGATATATGTTATTGATTCCAAGACAAAGTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G21600.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G21600.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g01890.1 (Oryza sativa), 3'ss of exon 3
-gttttttaagcattaaggatgagatcaacacgaaactactta-gtttagtagttacagtttctgatacaaattgtcttcatcgtgtttattttttatgcagGTTTTCTTGACAAAACATTACCGGAACAGAAGGACAAACGATCCAGAATTTGTGCTAGATCTTGAAGAGATATATGTTATTGATTCCAAGACAAAGTCAA
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tctacccaatatgctatctttcttat-accttaagagcatatatgctggactgttgttttcttcaaaatttat-atatgctccatatttgtttatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTTTTCCTTGATTTTGAAGAGATATATGTTATTGACTCGAAAGCAAGGTCAA
upper sequence: AT1G21600.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g01950.1 (Oryza sativa), 3'ss of exon 3
gttttttaagcattaaggatgagatcaacacgaaactacttagtttagtagttacagtttctgatacaaattgtcttcat--cgtgtttattttttatgcagGTTTTCTTGACAAAACATTACCGGAACAGAAGGACAAACGATCCAGAATTTGTGCTAGATCTTGAAGAGATATATGTTATTGATTCCAAGACAAAGTCAA
| |||| || | | | || | | | | | | | | | |||| | || || | | | | | ||| ||| | || |||||||||| |||||||||||| |||| || || ||||| ||||| ||| | || ||| |||||||||||||||||||||| || || ||| |||||
ctatttttagtttctacc-caatatgaccttaagaacatatgtgctgg-gtctgtggttttcttcaaaatttatatatgttccatatttgtttatgctgtagGTTTTCTTAACAAAACATTACAGGAATAGGCGGTGTAACGACCCAGATTTTTTCCTTGATTTTGAAGAGATATATGTTATTGACTCAAAAGCAAGGTCAA
upper sequence: AT1G21600.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G42430.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------gttttttaagcattaaggatgagatcaacacgaaactacttagtttagtagttacagtttctgatacaa-attgtcttcatcgtgtttattttttatgcagGTTTTCTTGACAAAACATTACCGGAACAGAAGGACAAACGATCCAGAATTTGTGCTAGATCTTGAAGAGATATATGTTATTGATTCCAAGACAAAGTCAA
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gtagttgtttcttgcatctttccttataggtattgtagtagaggaaatttcattataaatttgtagcaataagtccaagcatttgaaaaaaaattaacat--agttactgaaatga-tgctcttggtctttgctaaaatggctccctcatcagacttgtttcggttacagGTGTACTTGACAAAACACTACAAAAATAGGAGGAAGGGTGATCCTGAGTTTGTGCTAGATTTTGAAGAGATTTATGTTATCGATTCCAAAACCAAGTCAA
upper sequence: AT1G21600.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G12370.1 (Glycine max), 3'ss of exon 3
gttttttaagcatt--aaggatgagatcaacacgaaactacttagtttagtagttacagtttctgatacaa-attgtcttcatcgtgtttattttttat-gcagGTTTTCTTGACAAAACATTACCGGAACAGAAGGACAAACGATCCAGAATTTGTGCTAGATCTTGAAGAGATATATGTTATTGATTCCAAGACAAAGTCAA
| || |||| || | || || |||| | |||| | | | | | || | || || || | | |||| | || ||| | | ||||| | |||||||||||| ||| || |||||| ||| | || |||||||| ||| |||||||||| ||||||||||||||||| | |||||||
-aagtccaatcattgtaaaaaagaaattaacat--agttactgaaatga-tgctcttggtctttgctagaatgtctccctcataggacttctttcctgttacagGTGTACTTGACAAAACACTACAAAAATCGAAGGAAGGGTGATTCTGAGTTTGTGCTTGATTTTGAAGAGATTTATGTTATTGATTCCAAATCCAAGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtagttacagtttctgatacaaattgtcttcatcgtgtttattttttatgcagGTTTTCTTGACAAAACATTACCGGAACAGAAGGACAAACGATCCAGAATTTGTGCTAGATCTTGAAGAGATATATGTTATTGATTCCAAGACAAAGTCAA
ttctgat putative branch site (score: 3)
tttatttttt putative PPT
tgtttattttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttttaagcattaaggatgagatcaacacgaaactacttagtttagtagttacagtttctgatacaaattgtcttcatcgtgtttattttttatgcagGTTTTCTTGACAAAACATTACCGGAACAGAAGGACAAACGATCCAGAATTTGTGCTAGATCTTGAAGAGATATATGTTATTGATTCCAAGACAAAGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA