Sequence
atgc intronic sequence ATGC exonic sequence...ggaaccatgcattgtatccaagggtttgtatttgcagtttgtattattttatgctcactaccaaatttgcaggtattgaacttttcatccataatttcagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCTATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------ggaaccatgcattgtatccaagggtttgtatttgcagtttgtat---tattttatgctca------ctaccaaatttgcagg-----tattgaacttttcatccataatttcagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCTATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
| | ||| | ||| ||| ||| ||||| | | || | | ||| | | || || | | | || ||| || | | |||||||| |||||||| ||||| | ||||| ||||| || ||||||||| | | ||||||||||||||||||||| || ||||| |||||||| ||||| |
gtattttgttctccttcatgacacctttttataatgatttgtttctctctctctctctctctctctctctctcaatatattactttattctggtgaagtatttcagttt-cagttcatttacatacctagcagagaaaatatctatagactgtgaagaagtaattctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 2
--ggaaccatgcattgtatccaagg-gtttgtatttgcagtttgtattattttatgctcactaccaaatttgcaggtattgaacttttcatccataatttcagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCTATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
|| || | | || ||| || | || | || | | ||| || | | | | | || ||| || | | |||||||| |||||||| ||||| | ||||| ||||| || ||||||||| | | ||||||||||||||||||||| || ||||| |||||||| ||||| |
ctggtgaagtgtttcagtttcagttcatttacatgtctagcagagaaaatatc-tatagactgtgaagaaggaa--ttctaatattgccataaatgactgcagGTTGGGTACATTGTAACATCAAGTTTGCTTAATGAAAATCATGACTTTCTCAGGTTGGCTATAAATACAGTGCGCAATGATATCATTGGTCGTAATGAAA
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 2
ggaaccatgcattgtatc-caagggtttgtatttgcagtttgtattattttat--gctcactaccaaatttgcaggtattgaacttttcatccataatttcagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCTATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
|||| | | |||| | | | || || | | || | | ||| ||| | ||| || | | | | || | | ||||| || |||||||| || || || || ||||||||||||||||||||||||| ||| || |||||||| ||||| || ||||||||||| || ||||| |
--ttttgtgcagttcactgcaagtttattaactttcatcacattacaattggttggttcattac-acttttattaactttcatcatattataattggctgcagGTGGGGTACATTGTAACGTCATGTTTACTCAATGAGAACCATGACTTTTTGAGGTTAGCAATAAATACTGTGCGCAATGATATTATTGGCCGAAATGAAA
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 2
ggaaccatgcattgtatccaagggtttgtatttgcagtttgtattattttatgctcactaccaaatttgcaggtattgaacttttcatccataatttcagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCTATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
||| || || || | | || || || | |||| | | | ||| | || || || |||||||||||||| || ||||||||| |||||||||||||||| || |||||| ||| || || || || || || || || ||||||||||||||||
----gtatgtatcaaatatcgatattccttgcaaccgtcagtgac-ttgcctctgcactgttacact---gggtctaatgattggtattaat-----cagGTTGGCTACATCGTCACATCTTGCCTGCTCAATGAGAACCACGATTTTTTGCGACTGGTCATTAACACTGTCCGTAATGACATCATTGGTCGGAATGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttatgctcactaccaaatttgcaggtattgaacttttcatccataatttcagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCTATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
tgctcac putative branch site (score: 2)
ataatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaccatgcattgtatccaagggtttgtatttgcagtttgtattattttatgctcactaccaaatttgcaggtattgaacttttcatccataatttcagGTTGGCTACATTGTTACATCTTGCTTGCTCAATGAGAACCATGACTTTTTGAAGTTGGCTATAAATACAGTGCGGAACGATATTATTGGTCGGAATGAGA
ggaacca
- - - - - - - tatccaa
- - - - - - - - - - - ggtttgt
- - - - - - - - - - - - - - - - - -agtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - taccaaa