Sequence
atgc intronic sequence ATGC exonic sequencegtctgagacagattaagcatacttagctttttcttatgagaaacgttatgcatctttgtaactttgtgaatttttgtgcagTGACTTCTCGCATATTTTCGATGTTGATTGGTTTATCTCATTTCTGTCTGGAGACGTCAGAATTATAAAGCAACTTCCACTGAAAGGAGGGCGTACATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G76270.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G02010.1 (Glycine max), 3'ss of exon 5
---------------gtctgagacagattaagca-tacttagctttttcttatgagaaacgttatgcatctttgtaact-ttgtgaatt---------------tttgtgcagTGACTTCTCGCATATTTTCGATGTTGATTGGTTTATCTCATTTCTGTCTGGAGACGTCAGAATTATAAAGCAACTTCCACTGAAAGGAGGGCGTACATGG
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gtcagtcacaacagtggcacagattgcctgagcggtgtctgcacttttgctatt-gcaattttatgtggttatctgagtattgtgaaatgttgacatactttgctttttgcagTAACTTCTCAGAGATCTTTGATGTTGATTGGTTTATATCATTTCTGTCAAAAGATGTCAAAATTATCAAGCAACTTCCCACTAAGGGTAGGAAAGCATTA
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 4
-------------------------gtctgagacagattaagcatacttagctttttcttatgaga--aacgttatgcatctttgtaactttgtgaatttttg-----tgcagTGACTTCTCGCATATTTTCGATGTTGATTGGTTTATCTCATTTCTGTCTGGAGACGTCAGAATTATAAAGCAACTTCC-ACTGAAAGGAGGGCGTACATGG
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gtcagttacaatagttgcacagattgcctgag-cggtgtctgcacttttgctattgtaatttgaggtggttatcagagtactgtgaaatcttgacatactttgctttttgcagTAACTTCTCAGAGATCTTTGATGTTGATTGGTTTATATCATTTCTGTCAAAAGATGTCAAAATTATCAAGCAACTTCCTACTAAGGGTAGTAGGAAAGCA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttcttatgagaaacgttatgcatctttgtaactttgtgaatttttgtgcagTGACTTCTCGCATATTTTCGATGTTGATTGGTTTATCTCATTTCTGTCTGGAGACGTCAGAATTATAAAGCAACTTCCACTGAAAGGAGGGCGTACATGG
ttgtaac putative branch site (score: 2)
tttttgt putative PPT
tgaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgagacagattaagcatacttagctttttcttatgagaaacgttatgcatctttgtaactttgtgaatttttgtgcagTGACTTCTCGCATATTTTCGATGTTGATTGGTTTATCTCATTTCTGTCTGGAGACGTCAGAATTATAAAGCAACTTCCACTGAAAGGAGGGCGTACATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG