Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaacagagctttttaattaccggttaaatctggttcaccggttaatattggttattggttgttttttcagACCGTTGCACTTGTTGGAGAGAGCGGGAGCGGGAAATCAACGGTGATAAGCATGATTGAGAGGTTTTATAATCCAGATTCAGGCAAGATTTTGATCGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G18050.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g34970.1 (Oryza sativa), 3'ss of exon 11
-------------gtaaaaaacagagctttttaattaccggttaaatctggttcaccggt--taatattggtta---ttggttgttttttcagACCGTTGCACTTGTTGGAGAGAGCGGGAGCGGGAAATCAACGGTGATAAGCATGATTGAGAGGTTTTATAATCCAGATTCAGGCAAGATTTTGATCGATC
|| || || | | || | || | | | | | | | | || | || || ||| | || | |||||||| |||||||| |||||||||||||| |||||||| || |||| ||| || |||| ||||| || | || ||| | |||||||| | | |||
gttgctttctatctgaactaagtgaacatatttagtatcattaacacattgctagcttgtgttgatcttaattacattacattatggtttcagACTGTTGCACTGGTTGGAGAGAGCGGAAGCGGGAAGTCCACGGCGATTGCGCTGCTTGAAAGGTTCTACGACCCGGATACCGGCAAGATCCTTCTTGATG
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g50160.1 (Oryza sativa), 3'ss of exon 11
-gtaaaaaacagagctttttaattaccggttaaatctggttcaccggttaatattgg---ttattggttg--ttttttcagACCGTTGCACTTGTTGGAGAGAGCGGGAGCGGGAAATCAACGGTGATAAGCATGATTGAGAGGTTTTATAATCCAGATTCAGGCAAGATTTTGATCGATC
|| || | | || | |||| || | | || || | ||| | || ||| | |||||||||||||||||||||||||| || ||||| || || || | || || | ||| | || || ||||| || ||||| | || ||| | |||
gttatccaatttatatgcttgttgcatagttatattttctgcattaacatatccagcaacttactatatggatttatgcagACCGTTGCACTTGTTGGAGAGAGTGGTAGCGGAAAGTCCACAGCAATCGCTTTGCTAGAGCGATTCTACAATCCCGAGTCAGGAACCATCTTGTTGGATG
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g50080.1 (Oryza sativa), 3'ss of exon 9
------------------gtaaaaaacagagcttttta-----attaccggtta-aatctggttcaccggttaatattggttattggttgtt-ttttcagACCGTTGCACTTGTTGGAGAGAGCGGGAGCGGGAAATCAACGGTGATAAGCATGATTGAGAGGTTTTATAATCCAGATTCAGGCAAGATTTTGATCGATC
| || ||| | | | || ||| | ||| ||| | || | | |||| | | ||||| ||||||||||||||||||||||| || || || || || || || || | ||| | || ||| | ||| |||| |||| || | | ||
ctttcaaatgaaaattaccaataatacaaatttctctatatttattttcctttataattaaacttgtactgacatgctataaaccaattgtcatatgcagACTGTTGCACTTGTTGGAGAGAGCGGCAGTGGAAAGTCCACAGTAATTGCTTTGCTGGAGCGATTCTATGACCCACATTCTGGCACAATCTCACTAGACA
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv10s0003g02580.t01 (Vitis vinifera), 3'ss of exon 11
gtaaaaaacagagctttttaattaccggttaaatctggttcaccggttaatattggttattggttgttttttcagACCGTTGCACTTGTTGGAGAGAGCGGGAGCGGGAAATCAACGGTGATAAGCATGATTGAGAGGTTTTATAATCCAGATTCAGGCAAGATTTTGATCGATC
| | || | | | | || | | | || | | || | |||| ||| | ||||| || ||||||||||| || || ||||| ||||| ||||| ||| | || |||||||| |||||||| ||||| || || ||| | |||
--------gtaatcacttccactgctgcttgtcttttaactttcatttgct-tgacttgaaaatc--ttttgcagGCTGTTGCTCTAGTTGGAGAGAGTGGAAGTGGGAAGTCAACAGTGATCAGCCTAATAGAGAGGTTCTATAATCCTGATTCCGGGGCTATATTGTTGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaccggttaaatctggttcaccggttaatattggttattggttgttttttcagACCGTTGCACTTGTTGGAGAGAGCGGGAGCGGGAAATCAACGGTGATAAGCATGATTGAGAGGTTTTATAATCCAGATTCAGGCAAGATTTTGATCGATC
ttgttttttc CT-rich tract
ttaatattggttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaacagagctttttaattaccggttaaatctggttcaccggttaatattggttattggttgttttttcagACCGTTGCACTTGTTGGAGAGAGCGGGAGCGGGAAATCAACGGTGATAAGCATGATTGAGAGGTTTTATAATCCAGATTCAGGCAAGATTTTGATCGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA