Sequence
atgc intronic sequence ATGC exonic sequencegtttgttatttcttgttcttttataagttctttgttggtcttggtacttgagctgactagtggatatgcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50530.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 3
--------------gtttgttatttcttgttcttttataagttctttgttggtcttggtacttgagctgactagtggatatgcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
||| ||| || | || | | | ||| | || | || | | | || | |||| ||||| |||||||| || || |||||||| || ||||| || || || ||||| || || ||||| |||||||||||||||| || |||||||| |
gtgggtgaagtcccaaacactatctctggtcccttgtttgcacttctcttgattttcctga--gaatgtatcacttcat-tccagGTAAGTTCAGACATTTACCTGTCGTGGAGAACGGTGAAGTCATTGCACTGCTCGACATAGCCAAGTGCCTGTATGATGCTATTGCGCGAATGGAAAGGGC
upper sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G01470.1 (Glycine max), 3'ss of exon 2
-----------------------gtttgttatttcttgttcttttataagttctttgttggtcttggtacttgagctgactagtggatatgcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
|| || || | || | ||| | |||| | |||| || | | | || | | |||| | ||| |||||||| || ||||||||||||||||||||| | || | || || || |||||||||||||||||||| |||||||| ||||||||
gttggtattactcggagataggcacatgctaatttctatttctgtatggtgcc---attggaataagtaca-aagatcatttatg--ttttcagGGAGGTTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTGTTGCCATACTTGACATAGCAAAGTGTTTGTATGATGCCATTGCCCGTATGGAAAGGAA
upper sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G37370.3 (Glycine max), 3'ss of exon 4
---------gtttgttatttcttgttcttttataagtt-----ctttgttg-gtcttggtacttgagc---tgactagtggatat--gcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
|| | | ||| ||||| |||| || || || |||| || || | || | |||| || || |||||||| || ||||||||||||||||||||| | || | || || || |||||||||||| ||||||| |||||||| |||||||| |
gttggtagtgtatatagagaaacacaacttttcaagttagttacttttctgtatcctgccttttgaatacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
upper sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G38140.1 (Glycine max), 3'ss of exon 3
----------------gtttgttat-ttcttgttcttttataagttctttgttggtcttggtacttgagctgactagtggatatgcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
| | | | | || || | | | || | || | | || | || | | | | |||| | ||| |||||||| || |||||||||||||||||||| | || | || || || |||||||||||||||||||| |||||||| |||||||| |
gttggtattacacggagataggcacatgctaattactatttcggtacggtgccc-tttgaataaatacaaagatgattatgttttcagGGAGGTTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTAGTTGCCATACTTGACATAGCAAAGTGTTTGTATGATGCCATTGCCCGTATGGAAAGGGC
upper sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtttgttatttcttgttcttttataagttctttgttg-gtcttggtacttgagctgactagtggatat--gcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
| || ||| ||| | | | || | | |||| | ||| | | || | | ||||| ||||| ||||||||||| || || |||||||| || || || || | || || || ||||||||||| |||||||||||||| || ||||| || |
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
upper sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S86_24V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------gtttgttatttcttgttcttttataagttctttgttggtcttggtacttgagctgactagtggatatgcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
| ||| | | | || ||| | | | || | | | | ||| |||||||||| || |||||||| || |||||||||||||| ||| | || ||||| ||||| |||| ||| | || ||||||||||| |||||||| | |
ttgacttcattacgaatttcatgaaaataagcgtaaccatatattcctagtgtattgcaagatgacagcttctcatatattatatctcaatttgtga-----cagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTCTGGATATCACAAAATGTCTCTACGATGCTATTGCTCGCATGGAGCGGGC
upper sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S119_11V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------gtttgttatttcttgtt---cttttataagttctttgttggtcttggtac---ttgagctgactagtggatat-----gcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
|||||| | | | || | || | | | | | | || || | || | | ||| |||||||||| || |||||||| ||||||||||| ||||| ||| |||| ||||| ||||| | |||||| | |||||||||||||| |||||||| | |
caggtttatgtaaatcatccgtgttatgtacgactacgcagtttcagtgtcgtggaagatgtgagcacatcttaaactatcccatctctatttgtgacagGCAAGTTCAGGCATTTGCCTGTGGTGGAGAAGGGAGAGGTTGTCGCACTTCTGGATATCACCAAGTGTCTCTATGATGCTATTGCTCGCATGGAGCGGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttataagttctttgttggtcttggtacttgagctgactagtggatatgcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
agctgac putative branch site (score: 3)
tataagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttatttcttgttcttttataagttctttgttggtcttggtacttgagctgactagtggatatgcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA