Sequence
atgc intronic sequence ATGC exonic sequencegtatgtactcatattttatcaaggttattctctaagttcttatgctaatcatttacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18620.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
-------gtatg-tactcatatttt--atcaa--ggttattctctaagttcttatgctaatcatttacc---tcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
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gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
--------------gtatgtactca-tattttatcaaggttattctctaagtt--cttatgctaatcatttac-----ctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
| |||| | | || | | | || | | | | | ||||| | || ||| || ||||||| || |||||||||||||| ||| | ||||| ||||| || || || ||||| || |||||||| || || || || ||||| |||||||| ||||
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 8
----------gtatgtactcatattttatcaaggttattctctaagttcttatgctaatcatttacctcatcttt---gtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
| | | ||| | || | || || | | || | |||| ||| || |||| ||||||| || |||||||||||| ||||| | || || |||||||| || || ||||||| || ||||| || ||||| |||||||| |||||||| ||||
gttgggatataattatcatgataactaattatagtactttaaaatgaactcttaataattgtttcttgcaacttttgcaaagGTTCTTCGCCCATTTCTTCTTAGGAGGCTCAAGTCTGATGTAGAAAAGGGTCTACCTCCGAAGAAGGAAACCATACTTAAAGTTGGAATGTCTCAGATGC
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 8
----------gtatgtactcatattttatcaaggttatt--ctctaagtt--cttatgctaatcatttacctcatctttgta------gGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
| | | || | || | | || || ||| | | || | |||||| | | ||| |||| ||| || ||||||||||| ||||| ||||| || |||||||| |||||||| || || ||||||||||| || || || ||||| |||||||| |||||||
gtaaattacagaaccttcttttgattgttggaagtccttgatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGACCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGATTGCCACCAAAAAAGGAAACTATTCTTAAAGTAGGCATGTCCCAAATGC
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 8
---------gtatgtactcatatttta--tcaaggttattc--tctaagttcttatgctaatcatt-tacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
| | || || ||||| || | ||||| ||| | || | | | | || || ||| ||||| || || || || || |||||||| | || |||||||| ||||||||||| |||||||||||||| |||||||| ||||| |||||||||||| |||
gtaaacccaagacctcctaattttttagctctaccttatttcatctcatttactgaaatggtttctgtatttctgttttttagGTCCTCCGGCCTTTCCTCCTTCGGAGACTGAAGTCAGATGTTGAGAAAGGCTTGCCTCCAAAAAAGGAAACAATACTTAAAGTAGGCATGTCTCAATTGC
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtactcatattttatcaaggttattctctaa-gttcttatgctaatcatt--tacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
|| || || | || || || ||| || | | | || |||| | || |||||||| | | | | || || ||||| || | ||| ||||| ||||| ||||||||||| ||||||||||| |||||||| ||||
-----------------------gtacttatccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtactcatattttatcaaggttattctctaa-gttcttatgctaatcatt--tacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
|| || || | || || || ||| || | | | || |||| | || |||||||| | | | | || || ||||| || | ||| || || ||||| ||||||||||| ||||||||||| |||||||| ||||
-----------------------gtacttatccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTGCCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatcaaggttattctctaagttcttatgctaatcatttacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
tgctaat putative branch site (score: 2)
tttacctcatcttt putative PPT
taatcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtactcatattttatcaaggttattctctaagttcttatgctaatcatttacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA