Sequence
atgc intronic sequence ATGC exonic sequencegttcacttttatatccttctctcaaatgatgattttgttttggatatgtggtactttcctcgtgttcttactgtatgctctcctttattgctagACCCCTGAAGATGTTGACAAGCTTCGTAAAATTGGAGTTAAAACCATATTTTGCTTGCAACAAGATCCAGACCTGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G52180.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G52180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 5
gttcacttttatatccttctctcaaatgatgattttgttttgg-atatgtggtactttcctcgtgttcttactgtatgctctccttt--attgctagACCCCTGAAGATGTTGACAAGCTTCGTAAAATTGGAGTTAAAACCATATTTTGCTTGCAACAAGATCCAGACCTGGA
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--gtatttttg-attcaattatggatacctgattgaattctgtcaaatctagt-tttgccctgacttctatttttttgtttcccctcaaattaccagACTCCTGAAGATGTAGACAAGTTGTGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATCCAGACCTTGA
upper sequence: AT3G52180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G34370.1 (Glycine max), 3'ss of exon 5
gttcacttttatatccttctctcaaatgatgattttgttttgg-atatgtggtactttcctcgtgttcttactgtatgctctcctttattgctagACCCCTGAAGATGTTGACAAGCTTCGTAAAATTGGAGTTAAAACCATATTTTGCTTGCAACAAGATCCAGACCTGGA
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--gtattttt-tattcaattatggatacctgatcgaattctgtcaaatctagtttggtcctgacttctatttttttctctccctcaaattaccagACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA
upper sequence: AT3G52180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 5
--gttcacttttatatccttctctcaaatgatgattttgttttggatatgtggtactttcctcgtgttcttactgtatgctctcctttattgctagACCCCTGAAGATGTTGACAAGCTTCGTAAAATTGGAGTTAAAACCATATTTTGCTTGCAACAAGATCCAGACCTGGA
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gtgataccatttctactctttaattaggagaagtttttttcctttctaagaaga-------tcatttgatttttgtttttcctcc--aaatggcagAGTCCAGAAGATGTTGACAAGCTTCGGAGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggatatgtggtactttcctcgtgttcttactgtatgctctcctttattgctagACCCCTGAAGATGTTGACAAGCTTCGTAAAATTGGAGTTAAAACCATATTTTGCTTGCAACAAGATCCAGACCTGGA
ttcttac putative branch site (score: 2)
ctctcctttattgct putative PPT
tttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcacttttatatccttctctcaaatgatgattttgttttggatatgtggtactttcctcgtgttcttactgtatgctctcctttattgctagACCCCTGAAGATGTTGACAAGCTTCGTAAAATTGGAGTTAAAACCATATTTTGCTTGCAACAAGATCCAGACCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG