Sequence
atgc intronic sequence ATGC exonic sequencegtatgagtaatctttcatttaattagtaatctttccactcatgtcttagacaagttagtttcagttttatctgcaatttgggataactaaatgaaacctgtgaaaataaaggactgttctttaatcccttttgatctcagtacagAAACAACATTGAACAAGGTCGAAAAATCATCGTTGATGCTTGCTTACGAGGTTAACGCTGTTGGTCCAATTCTAGTGATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G20760.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G20760.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G14360.1 (Glycine max), 3'ss of exon 3
gtatgagtaatctttcatttaattagtaatctttccactcatgtcttagacaagttagtttcagttttatctgcaatttgggataactaaatgaaacctgtgaaaataaaggactgttctttaatcccttttgatctcagtacagAAACAACATTGAACAAGGTCGAAAAATCATCGTTGATGCTTGCTTACGAGGTTAACGCTGTTGGTCCAATTCTAGTGATGAAG
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-------------------------------------ttcatgt---aaaattgtgaaataaagtgcgatt---atcttgttttgagcttatgtttcttac--aaatacaaggcagttgattatatagttatctatacaatacagAAACAACATTGAACAAAGTGGAGAAATCATCTTTAATGCTTGCATATGAGGTTAATGCAGTGGGTCCTATCTTAGTTATCAAG
upper sequence: AT4G20760.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G03440.1 (Glycine max), 3'ss of exon 4
gtatgagtaatctttcatttaattagtaatctttccactcatgtcttagacaagttagtttcagttttatctgcaatttgggataactaaatgaaacctgtgaaaataaaggactgttctttaatcccttttgatctcagtacagAAACAACATTGAACAAGGTCGAAAAATCATCGTTGATGCTTGCTTACGAGGTTAACGCTGTTGGTCCAATTCTAGTGATGAAG
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------------------------------------------gatgtaaaattgtgagctaaagagctatt---atcttgttttgggtttatgtttcttataaatacaaggcagtttgataatatttgttatctattcaaaacagAAACAACATTGAACAAAGTGGAGAAATCATCTTTAATGCTTGCGTATGAGGTTAATGCAGTGGGTCCTATCTTAGTTATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaaacctgtgaaaataaaggactgttctttaatcccttttgatctcagtacagAAACAACATTGAACAAGGTCGAAAAATCATCGTTGATGCTTGCTTACGAGGTTAACGCTGTTGGTCCAATTCTAGTGATGAAG
ttttgat putative branch site (score: 4)
tcccttttgatctc CT-rich tract
tgaaaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagtaatctttcatttaattagtaatctttccactcatgtcttagacaagttagtttcagttttatctgcaatttgggataactaaatgaaacctgtgaaaataaaggactgttctttaatcccttttgatctcagtacagAAACAACATTGAACAAGGTCGAAAAATCATCGTTGATGCTTGCTTACGAGGTTAACGCTGTTGGTCCAATTCTAGTGATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT