Sequence
atgc intronic sequence ATGC exonic sequencegtacgcatatattgttggttcccgatggaatttgtaattctaaatttctgtgtggttataaaatcaacatcttgttaagttcaattaatatcttctgacagagtataatatgttagACCACAGGTTACTCGCATTTGAAAGTTTCTCTTCTTCAAGATTCGTTTGTGAGAGAATTATGGAATCAAATTGGAAAGAGAGTATATCTTGAAATGATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18525.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18525.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g00560.t01 (Vitis vinifera), 3'ss of exon 4
gtacgcatatattgttggttcccgatggaatttgtaattctaaatttctgtgtggttataaaatcaacatcttgttaagttcaattaatatcttctgacagagtataatatgttagACCACAGGTTACTCGCATTTGAAAGTTTCTCTTCTTCAAGATTCGTTTGTGAGAGAATTATGGAATCAAATTGGAAAGAGAGTATATCTTGAAATGATTC-------
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------------------------------gttatgaagtttaatct-tattgacttgcacaaataaacttttttc---ttgaattcttattta--gacagt------catttcaggctacagGTTATTCACATTTGAAAGTTTCTCTTCTCCAAGACTCATTTGTGCGGGAGGTATGGAACCGGGTTGGTAAACAAACATATCTGGAGATGGTGCATCCTTT
upper sequence: AT5G18525.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g00030.t01 (Vitis vinifera), 3'ss of exon 4
gtacgcatatattgttggttcccgatggaatttgtaattctaaatttctgtgtggttataaaatcaacatcttgttaagttcaattaatatcttctgacagagtataatatgttagACCACAGGTTACTCGCATTTGAAAGTTTCTCTTCTTCAAGATTCGTTTGTGAGAGAATTATGGAATCAAATTGGAAAGAGAGTATATCTTGAAATGATTC-------
|| | | | ||| | | | || | | || | || | || |||| ||| | ||||| || | || | |||||||| || |||||||||||||||||||| ||||| || |||||| | || ||||||| | |||| || | |||||| || ||| | |
------------------------------gttatgaagtttaatct-tattgacttgcacgaataaacttttttc---ttgaattcttattta--gacagt------catttcaggctacagGTTATTCACATTTGAAAGTTTCTCTTCTCCAAGACTCATTTGTGCGGGAGGTATGGAACCGGGTTGGTAAACAAACATATCTGGAGATGGTGCATCCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcaacatcttgttaagttcaattaatatcttctgacagagtataatatgttagACCACAGGTTACTCGCATTTGAAAGTTTCTCTTCTTCAAGATTCGTTTGTGAGAGAATTATGGAATCAAATTGGAAAGAGAGTATATCTTGAAATGATTC
ttctgac putative branch site (score: 2)
ttaagttcaattaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcatatattgttggttcccgatggaatttgtaattctaaatttctgtgtggttataaaatcaacatcttgttaagttcaattaatatcttctgacagagtataatatgttagACCACAGGTTACTCGCATTTGAAAGTTTCTCTTCTTCAAGATTCGTTTGTGAGAGAATTATGGAATCAAATTGGAAAGAGAGTATATCTTGAAATGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA