Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatctcccttcgtttaatctaattgcactggatctgatcgttttccgtagtagttcctcaagttctaggattttagtttcgattcggagcttgattgttgttgtgcgaaaatctgtagGAAATCGAAGTTGTATCGATTTGATAAAGATGGAAGTCAGTGGAAGGAGAGAGGTGCTGGTACTGTTAAGTTTTTGAAACATAGAGTTTCTGGGAAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G30060.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G30060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g06880.t01 (Vitis vinifera), 3'ss of exon 1
gtatgtatctcccttcgtttaatctaattgcactggatctgatcgttttccgtagtagttcctcaagttctaggattttagtttcgattcggagcttgattgttgttgtgcgaaaatctgtagGAAATCGAAGTTGTATCGATTTGATAAAGATGGAAGTCAGTGGAAGGAGAGAGGTGCTGGTACTGTTAAGTTTTTGAAACATAGAGTTTCTGGGAAGATT
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-----------------------gtaattctctcctcttagatcagtatctccattttttcccttgattctagggttttgtt------------cttgattgtactggt-------tttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAGAGGTGCTGGTAGTGTGAAGCTTTTGAAGCACAAAGAATCTGGCAAGGTC
upper sequence: AT2G30060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S115_20V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgtatctcccttcgtttaatctaattgcactggatctgatcgttttccgtagtagttcctcaagttctaggattttagtttcgattcggagcttgattgttgttgtgcgaaaatctgtagGAAATCGAAGTTGTATCGATTTGATAAAGATGGAAGTCAGTGGAAGGAGAGAGGTGCTGGTACTGTTAAGTTTTTGAAACATAGAGTTTCTGGGAAGATT
|| || | | | || | ||| | | || | ||| | ||||| |||| | || | ||| | || | | || ||||| | ||| |||||||||||||||| || |||| |||||||| |||||||||| |||| || ||| | || | || | |||| ||| ||
--------------------aaattatgtctatattctaggacttgatgccgcaacttattgtcgaattcggaatgtatagttaagatt-gaag--taatttattttatatggtttgatgcagGAAGGCTAAGCTGTATCGATTTGATAAGGAGGGAACACAGTGGAAAGAGAGAGGTGTTGGTCAGGTGAAGATCCTGGAGCACAAGACAACTGGAAAGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaggattttagtttcgattcggagcttgattgttgttgtgcgaaaatctgtagGAAATCGAAGTTGTATCGATTTGATAAAGATGGAAGTCAGTGGAAGGAGAGAGGTGCTGGTACTGTTAAGTTTTTGAAACATAGAGTTTCTGGGAAGATT
gcttgat putative branch site (score: 5)
attttagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatctcccttcgtttaatctaattgcactggatctgatcgttttccgtagtagttcctcaagttctaggattttagtttcgattcggagcttgattgttgttgtgcgaaaatctgtagGAAATCGAAGTTGTATCGATTTGATAAAGATGGAAGTCAGTGGAAGGAGAGAGGTGCTGGTACTGTTAAGTTTTTGAAACATAGAGTTTCTGGGAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA