Sequence
atgc intronic sequence ATGC exonic sequencegtttgttgtaataattcctggtatatatctctttgcttgtttgttatcaagattacttacctttgttcgtgtttatactacttcagAGTTGTGATCAACTACGATTTTCCAACTGGAGTTGAAGACTATGTCCACCGTATTGGGAGAACCGGTCGAGCTGGTGCAACTGGAGTTGCATTCACTTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06480.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0020g00470.t01 (Vitis vinifera), 3'ss of exon 6
--------gtttgttgtaataattc---ctggtatatatctctttgcttgtttgttatcaagattac--ttacct--ttgt-tcgtgtttatactacttcagAGTTGTGATCAACTACGATTTTCCAACTGGAGTTGAAGACTATGTCCACCGTATTGGGAGAACCGGTCGAGCTGGTGCAACTGGAGTTGCATTCACTTTC
|||| || | | ||| ||||||| || | || || | |||| | || || || | | | | || | | |||| || || |||||||| ||||| ||||||||| ||||||| || |||||||| || || ||||||| | ||||||||||| ||||| ||| ||| ||
tttatgtagtttctttgcaaatttcacatcattatatatgctattattgatt--ttgttgggattccctttgtctcattatcttggggtttccatgcctcagGGTCGTAATCAACTATGATTTCCCAACTGGAATTGAAGATTACGTCCACCGAATCGGACGAACCGGGAGGGCTGGTGCAACAGGAGTATCATACACATTT
upper sequence: AT3G06480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S138_142V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------gtttgttgt----aataattcctggtatatatctctttgcttgtttgttat-----caagattacttacctttgttcgtgtttatactacttcagAGTTGTGATCAACTACGATTTTCCAACTGGAGTTGAAGACTATGTCCACCGTATTGGGAGAACCGGTCGAGCTGGTGCAACTGGAGTTGCATTCACTTTC
| || | | || | || || || | | ||||| ||| | |||| | || || | | ||| |||| ||||||| ||||||||| | || || ||||||||||| ||||| ||||||||||| || || |||||| | || || ||||||||||| ||||| |||||| ||| |||
gtattattttcgcttatcattttaaacagttacttgt-tctgtctctgccgttggtccttattctttcgtgacatctgatttctgt--gtgtcaatactac--cagAGTTGTCGTAAATTATGATTTTCCAACGGGAGTCGAAGACTATGTTCATCGAATTGGGCGTACAGGCCGAGCTGGTGCCACTGGTCTTGCATACACGTTC
upper sequence: AT3G06480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S42_89V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------gtttgttgtaataattcctggtatatatctc-tttgcttgttt--gttatcaag-attacttacctttgttcgtgttta-tactact-tcagAGTTGTGATCAACTACGATTTTCCAACTGGAGTTGAAGACTATGTCCACCGTATTGGGAGAACCGGTCGAGCTGGTGCAACTGGAGTTGCATTCACTTTC
|| | | || || | | || | | |||| || || || || | | || || | || | | || | || | || |||||||||| | || || ||||| || || |||||||||||||| || ||||| ||||| | || ||||||||||||||||| || |||||| || |||
gtgtttacttctcccttaaattttattgctcattatgcttaccccatttgtccattatggtcattaatcactcctgacttatgattgcgtgtggtattgctatcagAGTTGTCGTGAATTATGATTTCCCTACGGGAGTTGAAGACTACGTTCACCGGATTGGACGGACAGGTCGAGCTGGTGCAACCGGGCTTGCATATACATTC
upper sequence: AT3G06480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ28593 (Selaginella moellendorffii), 3'ss of exon 8
gtttgttgtaataattcctggtatatatctctttgcttgtttgttatcaagattacttacctttgttcgtgtttatactacttcagAGTTGTGATCAACTACGATTTTCCAACTGGAGTTGAAGACTATGTCCACCGTATTGGGAGAACCGGTCGAGCTGGTGCAACTGGAGTTGCATTCACTTTC
| | || || | | | | ||| ||| || ||| | || ||||| | ||||| || | | |||||||| || |||||||| ||||| || || || || ||||| |||||||| ||||| | ||||| ||||||||||| ||||| | || ||||||
-gtaagcgaaacaaagc--gagacttgtctttttctttctttccctc------tgctgaccttcgagt-tgtttgtattgc---agAGTTGTCATTAACTACGACTTTCCCACCGGTGTGGAGGACTACGTCCACCGCATTGGTCGGACCGGCCGAGCTGGTGCCACTGGCCTGGCTCACACTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcttgtttgttatcaagattacttacctttgttcgtgtttatactacttcagAGTTGTGATCAACTACGATTTTCCAACTGGAGTTGAAGACTATGTCCACCGTATTGGGAGAACCGGTCGAGCTGGTGCAACTGGAGTTGCATTCACTTTC
tacttac putative branch site (score: 1)
ctacttc putative PPT
tttatacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttgtaataattcctggtatatatctctttgcttgtttgttatcaagattacttacctttgttcgtgtttatactacttcagAGTTGTGATCAACTACGATTTTCCAACTGGAGTTGAAGACTATGTCCACCGTATTGGGAGAACCGGTCGAGCTGGTGCAACTGGAGTTGCATTCACTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA