Sequence
atgc intronic sequence ATGC exonic sequencegtaaaataaaactctctccttacagtgaatgaggtctatgtttcttgtgcaagaagtaactaattttgggattgattagGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G07540.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G07540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G110309_T01 (Zea mays), 3'ss of exon 9
------gtaaaataaaactctctccttacag---tgaatgaggtctatgttt-cttgtgcaagaagta-actaatt---ttgggattg-------attagGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
||| | | | |||| ||| | || || | || || ||| || | | | | ||| | | |||| | |||||||||||||||||||||||||||| || || || || ||||| || || | || ||||| || || |||||||| | |||||||| || |||| |
tgcactgtacattgctgcattctctggtcagattttaacgatgactttgaaagtttgaacaggcaatggattaaccgtgtcgaaattgtggtgcgaacagGACAAATGGAAGACGCTGGTGCACACCGCGAGCATCTCGCCGCAGCAGCGGCGTGGCGAGCCGGTGCCTCAGGAGCTGCTCGACCGGGTCCTGGCGGCCC
upper sequence: AT1G07540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G063151_T01 (Zea mays), 3'ss of exon 8
----------gtaaaataaaactctctccttacagtg-aatgaggtctatgtttcttgtgcaagaagt-aactaatt---ttgggattg-------attagGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
| ||||| | | | | || | || || | ||| || | | | |||||| | | ||||| | |||||||||||||||||||||| |||||||| || || || ||||| || || | || ||||| || || |||||||| | |||||||| || |||| |
acctgttggcgactgcctgcgttctctggccaaattttgacgatggct-tggattttgaacaggcaatgaactaaccgtgtcgagattgtggtgcgaacagGACAAATGGAAGACGCTGGTACACACAGCGAGCATCTCGCCGCAGCAGCGGCGTGGCGAGCCGGTGCCTCAGGAGCTGCTCGACCGGGTCCTGGCGGCCC
upper sequence: AT1G07540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 9
---------gtaaaataaaactctctccttacagtgaatgaggtctatgtttcttgtgcaagaa--------gtaactaattt-----tgggattgattagGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
|||| |||| || | || | |||| ||| ||| | | || || | | | |||| ||| || | |||| |||||||| || |||||||||||||||||||||||||| || |||||||| || ||||| ||||| || || || || ||| |||| ||||| || |
ggaaccaaaagaaaagaaaaaggtcactttcattagtatgaccccta-atttagtatagaaaaaaggtatgagcatatgatttgggtatggaatagtgcagGATAAATGGAAAACACTGGTGCACACAGCAAGAATATCACCTCAGCAAAGGAGGGGAGAGCCTGTTCCCCAAGAACTTTTGGACAGGGTCCTAACTGCCC
upper sequence: AT1G07540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G06680.1 (Glycine max), 3'ss of exon 8
------------gtaaaataaaactctc---tccttac---agtga-atgaggtctatgtttcttgtgcaagaagtaact--aattttgggattgattagGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
||| | || ||||||| | | | ||| | | | || || || | | ||||||||| ||| |||| |||||||| || ||||||||||| ||||||||||| || ||||||||||| ||||| || ||||| || || || || ||| |||| ||| ||| |
actttgatgatcataattttggtcttcttagtccttacctaactcacatggcagacaaatgttttacatgtgatgtgatttaaattttggggttgtgcagGATAAATGGAAAACACTGGTGCACACGGCAAGAATATCCCCTCAACAAAGGAGGGGTGAACCTGTTCCCCAAGAACTTTTGGACAGGGTTCTAGTGGCCC
upper sequence: AT1G07540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G41210.1 (Glycine max), 3'ss of exon 12
------gtaaaataaaactctctccttacag---tgaatgaggtctatgtttcttgtgcaagaag------------taactaattttgggattgattag-
| || ||| | | || || ||| ||||| | | | || | || || | |||| || || || ||| || |||||||| || |||||||||||||||||||||||| | || |||||||| || ||||| ||||| || || || || ||| |||| |||||
tgtaaagaaagatagtgattggatcctaaagaaaagaacaaggtcactttcattagtatagaaaaaaggcatgagcatatatgatttgggtatggaatagTGCAGGATAAATGGAAAACACTGGTGCACACAGCAAGAATATCAGCTCAGCAAAGGAGGGGAGAGCCTGTTCCCCAAGAACTTTTGGACAGGGTCCTAAC-----
upper sequence: AT1G07540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G14760.1 (Glycine max), 3'ss of exon 9
----------------gtaaaataaaactctct-ccttacagtgaatgaggtctatgtttcttgtgcaagaagtaact--aattttgggattgatt--agGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
||| | ||| | ||| || ||| | | ||| | | || | | | ||||||| ||| |||| |||||||| || ||||||||||| ||||||||||| || || |||||||| ||||| || ||||| || || || || ||| |||| ||| ||| |
gaccacttagatgatcataattttggtctccttacctaactcacaatcacacggcagagaaatgttttacatgtgatttgatttttggggttgtgcacagGATAAATGGAAAACACTGGTGCACACGGCAAGAATATCCCCTCAGCAAAGGAGGGGTGAACCTGTTCCCCAAGAACTTTTGGACAGGGTTCTAGTGGCCC
upper sequence: AT1G07540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 9
---------------------gtaaaataaaactctctccttacagt-gaatgaggtctatgtttcttg-tgcaagaagtaactaattttgggattgattagGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
|| | | ||| | || | | | |||| | || || | | | |||| ||||| || ||||||| ||||| || ||||||||||| ||||||||||| || || |||||||| |||||||| ||||| ||||| ||| | || |||| ||||| || |
ccccaaagagcaatctgggttgttgttttaccatctttttttggatttgtatgattgaaaagtcatgtgacggcggggtttggtaatgttgggtatg--cagGACAAGTGGAAAACTCTGGTGCACACGGCAAGAATATCCCCTCAGCAAAGGAGGGGTGAGCCTGTTCCCCAGGAACTCCTGGATAGGGTCCTAACTGCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaatgaggtctatgtttcttgtgcaagaagtaactaattttgggattgattagGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
aactaat putative branch site (score: 2)
aagtaactaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaataaaactctctccttacagtgaatgaggtctatgtttcttgtgcaagaagtaactaattttgggattgattagGACAAATGGAAGACGCTGGTGCACACAGCAAGAATATCACCGCAACAAAGGAGAGGTGAGCCAGTTCCACAGGAGCTCTTAGACCGGGTACTAACGGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT