Sequence
atgc intronic sequence ATGC exonic sequence...aacgttctgcaatgctctccaaggttttggtagataagctaatggtgacaagtgtaaatgttgctatttcttgctcattggtgaaacttttgtgattcagGATGACTCTGAAACAGTAGCAATGATCAAGGAACTCTTAGAAACACGCATCAGACCAGCAGTTCAAGATGATGGTGGGGACATTGAGTATTGTGGGTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20970.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20970.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g06330.1 (Oryza sativa), 3'ss of exon 3
-aacgttctgcaatgctctccaaggttttggtagataagctaatggtgacaagtgtaaatgttgctatttcttgctcattggtgaaacttttgtgattcagGATGACTCTGAAACAGTAGCAATGATCAAGGAACTCTTAGAAACACGCATCAGACCAGCAGTTCAAGATGATGGTGGGGACATTGAGTATTGTGGGTTTG
|| | | | | | | | || || ||| | ||| | | ||| | | | | || ||||||| || |||| ||| |||||||| || || | | || || ||||| ||||||| ||||||||||||||||| |||||||| ||| | || ||||
taatggctcacctcgttttgcgta-tcttcctaatctcctcaatcccctcctcctcaaacacaccctaagtattttcacatatttttcctctatgccatagGATGATTCAGAAATAGTTGCAATGATAAAAGAGTTGCTGGAGACTCGCATTCGACCAGCTGTTCAAGATGATGGTGGTGACATTGAATATCGAGGATTTG
upper sequence: AT3G20970.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 2
-aacgttctgcaatgctctccaaggttttggtagataagctaatggtgacaagtgtaaatgttgctatttcttgctcattggtgaaacttttgtgattcagGATGACTCTGAAACAGTAGCAATGATCAAGGAACTCTTAGAAACACGCATCAGACCAGCAGTTCAAGATGATGGTGGGGACATTGAGTATTGTGGGTTTG
|| | || || |||||| || | || | | | |||| | | || | || | | | | |||| || ||||||| ||||||||||| ||||||||||||||| | ||||| || || || |||| ||||| ||||||||||| ||||||||||| ||| | || ||||
taagactttgtaaaatggtccaagtttgtcttactcatggagtacataggaagtttgagaag-gcgaaaactaaatggtacatatacatttttccatatagGATGATTCTGAAACAGTTGCAATGATCAAGGAATTGTTAGAGACTCGAATTCGACCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTG
upper sequence: AT3G20970.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 3
-aacgttctgcaatgctc--tccaaggttttggtagataagctaatggtgacaagtgtaaatgttgctatttcttgctcattggtgaaacttttgtgattcagGATGACTCTGAAACAGTAGCAATGATCAAGGAACTCTTAGAAACACGCATCAGACCAGCAGTTCAAGATGATGGTGGGGACATTGAGTATTGTGGGTTTG
|| |||| | | | | | || ||| || || | || | | | | | | |||| | | ||| |||||||| |||||||| |||||||||||||| ||||| || || || || || ||||||||||||||||||||||||||||||| |||||| | || ||||
tggaactccaaaatgtttaattccaaatattttctgattgtctg-cagttattcctgcataaatctcatgtatataaccatttcttgtgttgccatga--cagGATGATTCTGAAACTGTAGCAATGATCAAAGAACTGTTGGAGACTCGTATTCGACCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacaagtgtaaatgttgctatttcttgctcattggtgaaacttttgtgattcagGATGACTCTGAAACAGTAGCAATGATCAAGGAACTCTTAGAAACACGCATCAGACCAGCAGTTCAAGATGATGGTGGGGACATTGAGTATTGTGGGTTTG
cttttgt CT-rich tract
taaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacgttctgcaatgctctccaaggttttggtagataagctaatggtgacaagtgtaaatgttgctatttcttgctcattggtgaaacttttgtgattcagGATGACTCTGAAACAGTAGCAATGATCAAGGAACTCTTAGAAACACGCATCAGACCAGCAGTTCAAGATGATGGTGGGGACATTGAGTATTGTGGGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - -tctccaa
- - - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - -aagctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaact