Sequence
atgc intronic sequence ATGC exonic sequence...cattacacgtcagcaaatgaaacttgtggttaagataactccaaaaaatgagatctaatttagtatgatttgctacatgtatgatgtctcaatgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G48230.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 8
-cattacacgtcagcaaatgaaa--cttgtggttaag-ataactccaaaaaatgagatctaatttagtatgatttgctacatgtatgatgtctcaatgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG
|| | | || || |||| | || | || || || | | || | | | ||| || | | || |||| | ||| ||||||| | | ||| ||| ||| ||||||||||||||||| |||||||| || |||||||| ||||| ||||| ||||| |||||
gttctaaaagcttgccaaggaaaagatcacatttgaacatttctgtaatattttagtgccataatggtactatgtaatttgatcattatgtgcc----tcttagTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG
upper sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 8
-----------------------------------cattacacgtcagcaaatgaaactt---gtggttaagataa-ctccaaaaaatgagatctaatttagtatgatt-tgctac--atg---tatgatgtctca-atgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG
||| | | | | || | ||| ||||| | | | | | || | || | || |||||| | ||| ||| | || ||| | ||| ||||||| | |||||| ||| |||||| || || |||||||| |||||||| || || ||||||||||||||||| ||||| |||||
gtaaatttcctcatgcaacaaagacataagactggcat-gccctttaattcattattcttcctatggttgcaacaggcctccttacatagggacttgtgcag-atgattattttactgatgccatgcaatttcttgtgtctcttagTTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG
upper sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
---cattacacgtcagcaaatgaaacttgtggttaagataactccaaaaaatgagatctaatttagtatgatttgctacatgtatgatgtctca-atgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG
|| | | ||||| ||| | | | | || | | | | ||| | |||| | ||| || || ||||| ||||||| | | |||| | | |||||| || || |||||||| |||||||| || || ||||||||||||||||| ||||| |||||
atgcaacgttccttgcataatgagctttgctagcag--ttatttgtaagatcaatgcatgac--agttttatttatgtcttgtgctattccttttgtgtcttagTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG
upper sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 6
--cattacacgtcagcaaatgaaacttgtggttaagataactccaaaaaatgagatctaatttagtatgatttgctacatgtatgatgtc-tcaatgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG
|| | | | || ||||| ||| | | | | | || | | || ||| | |||| || ||||| || || | | ||| ||||||| | | ||| | | |||||| || || |||||||| |||||| | || || ||||||||||||||||| ||||| |||||
tgcaacatcccttagataatgagctttg--ataacagttattgtaagat-caatgcatatggcagtttaatttatgacttgtattatttcctttctctcttagTTTGACCCAGTAAAGCTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATTGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgagatctaatttagtatgatttgctacatgtatgatgtctcaatgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG
atctaat putative branch site (score: 3)
taatttagtatgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattacacgtcagcaaatgaaacttgtggttaagataactccaaaaaatgagatctaatttagtatgatttgctacatgtatgatgtctcaatgtctcagTTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - cagcaaa
- - - - - - - - -tgaaact
- - - - - - - - - - - - - - - -aagataa
- - - - - - - - - - - - - - - - - - - - -caaaaaa