Sequence
atgc intronic sequence ATGC exonic sequencegtaggtccttttcttattctctccctctcttggttgttcttcttcttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G47550.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os03g42750.2 (Oryza sativa), 3'ss of exon 20
----------------------------------gtaggtccttttcttattc--tctccctctcttggttgttcttcttcttcccaatt---gttcatac---ttccctaaccattttttttct------tgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
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gttatgtttctttcttgtgttgttcattaatcttctcaatcttttttgcatgaggtcttttttgtttgtatgtttggcacctcatcattttgtggatatacaggtgactaaactattatgtgtctgttggatgcagTCTTTATGACTTGGCTAATGTTGTGCCAACTCTTGCAAAATTCTACCATGAGGCCAGTGAATCATATGAACAAGCTTGCACTCGTCATATCAGTTCACTT
upper sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 20
---------gtaggtccttttcttattctctccctctcttggttgttcttcttcttcccaattgttcatacttccctaac-catttttttt--cttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
| || | | | | ||| | | | | | | | ||| | | | | ||| || | | ||||| ||||| || | || |||||||| || || | || |||| ||||||||| || |||||||| |||||||||||||| | |||||||| | | |
ggccgaaaaaaaactctacccaacagaatttgctatacttacgaggacctagtggcctgtactactcacattaacttggtacatgttgtatgatatgcagTCTGTACGATTTAGCAAATGTTGTACCAACACTTGCTAAGTATTATCACCAAGCTAGTGAAGCTTATGAACAAGCTTGCTCACGCCACATCAATTTAGTC
upper sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 20
---------------------------------gtaggtccttttcttattctctccctctctt--ggttgttcttcttcttcccaattgttcatacttccctaaccattt--tttttcttgc--agCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
| | || || ||||| | | | || ||| ||||| | | | || ||| || | |||| || || |||| || |||||||||| || ||||| || || ||||| || ||||||||||| ||||| |||||||| || || |||||||| || ||||| ||||| ||||
gtaatgtttacgcatcaccctgccaaatggaggctcgaggctgtttcaattcttccattttttttaggtaattctttatacacagacaaagatatttttcacttattattttgttctttttgctcagTTTGTATGACCTTGCAAATGTCGTTCCCACTTTGGCGAAGTTTTATCATCAGGCTAGTGAAGCCTACGAGCAAGCTTGCACACGCCATATTAGTGTGATT
upper sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
---gtaggtccttttcttattctctccctctcttggttg-ttcttctt----cttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
| | | ||| || || | ||||| || | |||||||| ||| |||| | | | || | |||| ||||| |||||||||| || |||||||| || ||||||||||| || ||||||||||| |||||| | |||||||||||||| | ||| || |||||||||||
gtatttgtttatttattttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgattac-agacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttcttcttcttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
ccctaac putative branch site (score: 2)
cttccctaaccatttt CT-rich tract
taaccatttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtccttttcttattctctccctctcttggttgttcttcttcttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT