Sequence
atgc intronic sequence ATGC exonic sequencegtatttgttttctgcgatacatttcccttgaaccttttctgtctcgtgatcgggttttttccatggttgatatcgttttccaatctcagTATGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18480.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA09G31920.1 (Glycine max), 3'ss of exon 17
gtatttgttttctgc--gatacatttccct---tgaaccttttctgtctcgtgatcgggttttttccatggttgatatcgttttccaatct------cagTATGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAA
|| ||| ||| ||| | |||| | || | | ||| | | | | |||| || | | || ||| || | ||||||| ||||||||||||||||| |||| || ||||| ||||| ||||||||||| || || || ||||| || || |||||||| |||||||| ||||
gtttttaatttgtgcttaaaacatcactctatttcattcttcaagataacttttttcccttttaccctgaactcagatttatttgtgattttttgttcagTATGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA07G09890.3 (Glycine max), 3'ss of exon 15
-----gtatttgttttctgcgatacatttcccttgaaccttt-------tctgtctcgtgatcgggttttttccatggttgatatcgttttccaatctcagTATGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAA
|| |||| | |||| || | ||| || | || | | || | || | | || | ||||||| ||||||||||||||||| ||| || ||||| ||||| ||||||||||| || || || ||||| || || |||||||| |||||||| ||||
gtttttaatgtgttcttaaaacatcattctatttcagtcttcaagataacctttttcccttttaccctgaactcaagatttgtttgtgattatatgtacagTATGCTGAAGATCTTGAAAGTGGTTTCGCGTCAGATGTTGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAA
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 15
gtatttgttttctgcgatacatttcccttgaaccttttctgtctcgtgatcgggttttttccatggttgatatcgttttccaat-ctcagTATGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAA
|||| | | | || || || || | |||| || | ||| | || || | ||| || |||| || ||||||||||| ||||| |||||||| ||||| ||||| || |||||||| || || || ||||| || || || ||||| || ||||| ||||
gtatcttatcgcaattctatgctta--ttaaattatggttgtc-----atttcctctttcttaaatttcatcttctttaatcatgttcagCATTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAA
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: EFJ26077 (Selaginella moellendorffii), 3'ss of exon 15
gtatttgttttctgcgatacatttcccttgaaccttttctgtctcgtgatcgggttttttccatggttgatatcgttttccaatctcagTATGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAA
||||| | | | | ||| || | || | ||| |||| | | || ||||| ||| |||| | ||| ||| | ||||| || |||||||||||||||||||||||||| |||||||| || || || || | ||
---------------------------------gttttccataatttttt---actctttttttgtctaatgtttacacgtaat-tcagAAAATCGATGATCTGGAAGGTGGCATGGTCTCAGATATTGAATCGAAGTACAAGAAAATTTACGAAGATGACATAAACCCTTTCGCTGCGTTTTCAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctgtctcgtgatcgggttttttccatggttgatatcgttttccaatctcagTATGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAA
ggttgat putative branch site (score: 5)
tcgttttcc CT-rich tract
tttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgttttctgcgatacatttcccttgaaccttttctgtctcgtgatcgggttttttccatggttgatatcgttttccaatctcagTATGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG