Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtctaaggttctttaggtgattgattttgttatgtgtagttttatattgaaattgacacattttgctttgtagAAGGGAGAGATCATATAAGGTGGCAATCAAGTTTGTTGCACGGGCAAATATGCATCACTTAGGCGAGTTTCTAGCTGGTAAACGGGCAGATTGTCCGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43810.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtaagtgtctaaggttctttaggtgattgattttgt---tatgtgtagttttatattgaaattgacacatt--ttgctttgtagAAGGGAGAGATCATATAAGGTGGCAATCAAGTTTGTTGCACGGGCAAATATGCATCACTTAGGCGAGTTTCTAGCTGGTAAACGGGCAGATTGTCCGCAA
||| || ||| | | ||| ||||| | || ||| || | || || ||||||||| |||| |||||||| ||| || | ||||| |||||||||||||| ||||||||| || ||||||| ||| | |||||||||||||| || || ||| ||||||
gtaaggatttattgcatataatcactttaaatattttattttcttctctctcccccctctactcacacacacacaggcaaactccttttgtgtactagtataaccagataaaattgaacagttttgaatgtttgagtaagttcaattttcaactgacacattggccacttttcagAAGGGAAAGAGAGTACAGGGTGGTGATCAAGTTTGTTGCTCGGGCAAATTTGTATCACTTGGGCCAATTTCTAGCTGGTAAGCGTGCTGATGCACCGCAA
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------gtaagtgtctaaggttctttaggtgattgattttgttatgtgtagttttatattgaaattgacacattttgctttgtagAAGGGAGAGATCATATAAGGTGGCAATCAAGTTTGTTGCACGGGCAAATATGCATCACTTAGGCGAGTTTCTAGCTGGTAAACGGGCAGATTGTCCGCAA
||| |||| | | ||| || || | || ||| || | ||| | ||| | | ||| ||| |||||||| ||| |||| |||| |||||||||||||| |||| ||| |||| ||||| ||| |||||||||| |||||| | || || ||| |||
gtaagatttattattgcatagtaatttcatacttctatttggcttcaacacataagcatggtggactatatgtatgtgtgtgtgtgtctctatatgcat--ttgaattaagttcaatttccaactgacacttgcac----catttttcagAAGGGAAAGAGATTATAGAGTGGTGATCAAGTTTGTTGCCAGGGCCAATTTGCACCACTTGGGCCAGTTTCTAGCGGGTAAATGTGCTGAAGCTCCACAA
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtaagtgtctaaggttctttaggtgattgattttgttatgtgtagtt-ttatattgaaattgacac--attttgctttgtagAAGGGAGAGATCATATAAGGTGGCAATCAAGTTTGTTGCACGGGCAAATATGCATCACTTAGGCGAGTTTCTAGCTGGTAAACGGGCAGATTGTCCGCAA
||| | | | | | || | | | ||| || | || ||| | || || | | ||||| ||||| ||||| |||| ||||||||||| |||||||||| ||||||| || ||| ||||||| |||||||| || |||||| ||| ||
ccttgcccgttcattttttctgttgtatttgttgcaatgtgtctctcttccatctgtgtatatctgttgaattaattccaacctctatacaattcttcagAAGAGAGAGGGAGTATAAAGTGGTCATCAAGTTTGTAGCACGGGCAAGCTTGCATCATTTGGGCCAGTTTCTGGCTGGTAAGCGAGCAGATGCTCCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgattttgttatgtgtagttttatattgaaattgacacattttgctttgtagAAGGGAGAGATCATATAAGGTGGCAATCAAGTTTGTTGCACGGGCAAATATGCATCACTTAGGCGAGTTTCTAGCTGGTAAACGGGCAGATTGTCCGCAA
aattgac putative branch site (score: 3)
ttttgcttt putative PPT
tagttttatattgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtctaaggttctttaggtgattgattttgttatgtgtagttttatattgaaattgacacattttgctttgtagAAGGGAGAGATCATATAAGGTGGCAATCAAGTTTGTTGCACGGGCAAATATGCATCACTTAGGCGAGTTTCTAGCTGGTAAACGGGCAGATTGTCCGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT