Sequence
atgc intronic sequence ATGC exonic sequencegtttgcagacaatctttaacacaccatgttgacaatgtgcaagtttattgtaatcatgagtaacaaatttcatcttgcagCTCGTTTCTTGGGAAGAAGGTGGCTACAGAATTTCAGATAAACCAATGCCTAGAGGGGAGATTGTGGTAGGTGGTAACAGTGTAACAGCAGGTTACTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G04350.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G04350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 8
-----------------------gtttgcagacaatct--ttaacacaccatgttgacaatgtgcaagtttattgtaatcatgagtaacaaatttcatcttgcagCTCGTTTCTTGGGAAGAAGGTGGCTACAGAATTTCAGATAAACCAATGCCTAGAGGGGAGATTGTGGTAGGTGGTAACAGTGTAACAGCAGGTTACTTCA
||| ||| | | || | | ||||||| || || | | || | | | | | || | || ||||||||||| ||||||||||||||||| | |||||| ||| |||||||| |||| ||| |||| || ||||| |||| ||||| |||||| ||||
tttattagcaagcatttcattctgttgtgagatatttctgttctcttatcatgttgt--atatgtatctctaattctcttttttctgatcaaatgaatt---cagCTCGTTTCATGGGAAGAAGGTGGCTATAAAATTTCTGATTCTCCAATGCCCCGAGGAGAGGTTGTAGTTGGTGGATACAGCATAACAAAAGGTTATTTCA
upper sequence: AT2G04350.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 8
-------gtttgcagacaatctt--taacacaccatgttg--acaatgtgcaagtttattgtaatcatgagtaacaaa---------tttcatcttgcagCTCGTTTCTTGGGAAGAAGGTGGCTACAGAATTTCAGATAAACCAATGCCTAGAGGGGAGATTGTGGTAGGTGGTAACAGTGTAACAGCAGGTTACTTCA
|| ||| ||| | || | ||| | ||| | || | || | || | ||| | |||||||| |||||||||||||||||||| || | | || || ||||||||||| |||| ||| |||| || || || | ||| |||| || || ||||| |
agtttttgtacgcattcaagcacagtagtgtttccagttagaataattcgaggattgagaaccatttttctcaatggacatgtttggtttgacattgcagCTTGTTTCTTGGGAAGAAGGTGGGTATAAGACATCTGACAAACCAATGCCCCGAGGAGAGGTTGTAGTCGGGGGGTATAGTATAACTGCTGGCTACTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttgacaatgtgcaagtttattgtaatcatgagtaacaaatttcatcttgcagCTCGTTTCTTGGGAAGAAGGTGGCTACAGAATTTCAGATAAACCAATGCCTAGAGGGGAGATTGTGGTAGGTGGTAACAGTGTAACAGCAGGTTACTTCA
gagtaac putative branch site (score: 2)
tttcatctt putative PPT
aagtttattgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcagacaatctttaacacaccatgttgacaatgtgcaagtttattgtaatcatgagtaacaaatttcatcttgcagCTCGTTTCTTGGGAAGAAGGTGGCTACAGAATTTCAGATAAACCAATGCCTAGAGGGGAGATTGTGGTAGGTGGTAACAGTGTAACAGCAGGTTACTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT