Sequence
atgc intronic sequence ATGC exonic sequencegcaagtatatgatgatccacttctttactcctcctgtcaacggtaaaatgattcgtgttttgattagtagccaaactcataattggtattctctatgattggtgttgagcagGATGGATTGTTAGTTCTCTGCTTGCTGGTGCTACGGTAGGTTCATTCACTGGAGGTGCATTAGCTGACAAATTTGGACGAACAAGAACTTTTCAATTGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16150.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 4
gcaagtatatgatgatccacttctttactcctcctgtcaacggtaaaatgattc-gtgttttgattagtagccaaact-cataattggtattctctatgattggtgttgagcagGATGGATTGTTAGTTCTCTGCTTGCTGGTGCTACGGTAGGTTCATTCACTGGAGGTGCATTAGCTGACAAATTTGGACGAACAAGAACTTTTCAATTGGA
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----gtctaagaaaaacagctaaatcaaacatagaaa-gttgatagtatgattctatgagatattcgtttgcaatatttcacaat--gcattttgtttgtctctt-------agGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA
upper sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 4
gcaagtatatgatgatccacttctttactcctcctgtcaacggtaaaatga-ttcgtgttttgattagtagccaa--actcataattggt-attctctatgattggtgttgagcagGATGGATTGTTAGTTCTCTGCTTGCTGGTGCTACGGTAGGTTCATTCACTGGAGGTGCATTAGCTGACAAATTTGGACGAACAAGAACTTTTCAATTGGA
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----------------gaattttgtaattacatttgtccatgtgaatcttccttcactttcatatcccctatcaattgttttctcttggttatcatgagtgaatatctgtgaacagGCTGGATTGTCAGCACACTACTTGCTGGTGCCACTGTTGGTTCATTTACTGGTGGATCATTGGCTGACCAATTTGGAAGAACTAGGACTTTTCAATTAGC
upper sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 4
gcaagtatatgatgatccacttctttactcctcctgtcaacggtaaaatgattcgtgttttgattagtagccaaactcataattggtattctctatgattggtgttgagcagGATGGATTGTTAGTTCTCTGCTTGCTGGTGCTACGGTAGGTTCATTCACTGGAGGTGCATTAGCTGACAAATTTGGACGAACAAGAACTTTTCAATTGGA
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--------at-atattctatgttttcatttattttattttatttttattttttttatcaccaatgaatatctagctttacaa---gatttgacaatggagcattttgagcagGATGGGTTGTTAGCACACTCCTGGCTGGTGCCACTCTTGGTTCATTTACTGGTGGTGCATTGGCTGATAAATTTGGCAGAACAAGGACTTTTCAACTAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgattagtagccaaactcataattggtattctctatgattggtgttgagcagGATGGATTGTTAGTTCTCTGCTTGCTGGTGCTACGGTAGGTTCATTCACTGGAGGTGCATTAGCTGACAAATTTGGACGAACAAGAACTTTTCAATTGGA
ttttgat putative branch site (score: 4)
tcataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtatatgatgatccacttctttactcctcctgtcaacggtaaaatgattcgtgttttgattagtagccaaactcataattggtattctctatgattggtgttgagcagGATGGATTGTTAGTTCTCTGCTTGCTGGTGCTACGGTAGGTTCATTCACTGGAGGTGCATTAGCTGACAAATTTGGACGAACAAGAACTTTTCAATTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC