Sequence
atgc intronic sequence ATGC exonic sequencegtaaagagttcagcttctaagctctgtatcataggatcaccgttgatgttgtagaatgcaatgttttgaacttatacaacgttaatgaaacagGGTGTAGTTGTTTTCCATGACGTATTTGACAATGAACAAAATGTGGGTGGTGCCCAAATAAATCTGGAAGGTGTATATATATGGCCCTTTAGACAACTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28370.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G13220.1 (Glycine max), 3'ss of exon 3
-----gtaaagagttcagcttctaagctctgta---tcataggatcaccgttgatgttgtagaatgcaatgttttgaacttatacaacgttaatgaaacagGGTGTAGTTGTTTTCCATGACGTATTTGACAATGAACAAAATGTGGGTGGTGCCCAAATAAATCTGGAAGGTGTATATATATGGCCCTTTAGACAACTCC
|| | | || || | | || | | |||| || || | | | || || ||| | | | | || | ||||| ||||| | |||||||| ||||||||||||||| | ||||| ||||| || ||||| | | |||||||||||||||||||| | ||| || || |
cattaaacaataatacatatttttattgatgaaaatttatagactcggtcatgttaacttctcacaaaaataatttctctt-tgttatgcttatttatcagGGGGTAGTCATATTCCATGATGTATTTGACAATGAATACAATGTTGGTGGAGCTCAAATCAGAGTAGAAGGTGTATATATATGGCCTTATAGGCAGCTTC
upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G44530.1 (Glycine max), 3'ss of exon 3
--gtaaagagttcagcttctaagctctgta------tcataggatcaccgttgatgttgtagaatgcaatgttttgaacttatacaacgttaatgaaacagGGTGTAGTTGTTTTCCATGACGTATTTGACAATGAACAAAATGTGGGTGGTGCCCAAATAAATCTGGAAGGTGTATATATATGGCCCTTTAGACAACTCC
|||| | || | | | | || | |||| ||| || | | || || | | | | | | || | ||||| ||||| | |||||||| ||||||||||||||| | ||||| ||||| || ||||| | | |||||||| ||||||||||| | ||| || || |
gattaaacaattatacatttttgtattgatgaaagtttatagattcagtcatgtcaacttctcacaaaa-attatatctctttgttatgcttatttatcagGGGGTAGTCATATTCCATGATGTATTTGACAATGAATACAATGTTGGTGGAGCTCAAATCAGAGTAGAAGGTGTGTATATATGGCCATATAGGCAGCTTC
upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G37150.1 (Glycine max), 3'ss of exon 3
----gtaaagagttcagc----ttctaagctctgtatca-taggatcaccgttgatgttgtagaatgcaatgttttgaacttatacaacgttaatgaaacagGGTGTAGTTGTTTTCCATGACGTATTTGACAATGAACAAAATGTGGGTGGTGCCCAAATAAATCTGGAAGGTGTATATATATGGCCCTTTAGACAACTCC
| | |||| | | | ||| ||| || || | | || | || || || |||| | || ||| | || || | || ||||| |||||| | |||||||| || ||||||||||| | |||| || ||| | ||||| | | |||||||||||||||||||| |||||||| || |
attttttagattttcaatcatgtctttattagtgtttcaataaaataatccttattcttctataa--caatttattcctctttttcatgtttttttaatcagGGGGTAGTTATATTCCATGATGTGTTTGACAATGAGTATGATGTTGGCGGTTCTCAAATCAGAATAGAAGGTGTATATATATGGCCTTTTAGACAGCTTC
upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G33270.1 (Glycine max), 3'ss of exon 2
----gtaaagagttcagc----ttctaagctctgtatca-taggatcaccgttgatgttgtagaatgcaatgttttgaacttatacaacgttaatgaaacagGGTGTAGTTGTTTTCCATGACGTATTTGACAATGAACAAAATGTGGGTGGTGCCCAAATAAATCTGGAAGGTGTATATATATGGCCCTTTAGACAACTCC
| | |||| | || | |||| ||| || || | | || | || || || |||| | || ||| | || || | || ||||| |||||| | |||||||| || ||||||||||| | |||| || ||| | ||| | | | |||||||||||||||||||| |||||||| || |
aaattttagactttcaatcatgtccttattactgtttcaataaaataatccttattcttctataa--caatttattcctctttttcatgtttttttaatcagGGGGTAGTTATGTTCCATGATGTGTTTGACAATGAGTATGATGTTGGCGGTTCTCAAGTCAGAATAGAAGGTGTATATATATGGCCTTTTAGACAGCTTC
upper sequence: AT4G28370.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0028g03410.t01 (Vitis vinifera), 3'ss of exon 3
------gtaaagagttcagcttctaagctctgtatcataggatcaccgttgatgttgtagaatgcaatgttttgaacttatacaacgttaatga-aacagGGTGTAGTTGTTTTCCATGACGTATTTGACAATGAACAAAATGTGGGTGGTGCCCAAATAAATCTGGAAGGTGTATATATATGGCCCTTTAGACAACTCC
| ||| | | | | | | | | | ||| || | | | || ||||| | | | || || ||| || |||| || || | |||||||| || |||||||||||||| | || |||||| | ||||| | | |||||||||||||||||||| ||||||||||| |
ggagcatttttcagtgtaacatatgattttcctgccctttatcttttcctgaagtgctttatggtaaagttttatttctttgctacattgttgacaatagGGGGTGATTATATTCCATGATGTGTTTGACAATGAACATGAAGTTGGTGGTTCTCAAATCAGGGTAGAAGGTGTATATATATGGCCTTTTAGACAACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accgttgatgttgtagaatgcaatgttttgaacttatacaacgttaatgaaacagGGTGTAGTTGTTTTCCATGACGTATTTGACAATGAACAAAATGTGGGTGGTGCCCAAATAAATCTGGAAGGTGTATATATATGGCCCTTTAGACAACTCC
cgttaat putative branch site (score: 4)
ttaatgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagagttcagcttctaagctctgtatcataggatcaccgttgatgttgtagaatgcaatgttttgaacttatacaacgttaatgaaacagGGTGTAGTTGTTTTCCATGACGTATTTGACAATGAACAAAATGTGGGTGGTGCCCAAATAAATCTGGAAGGTGTATATATATGGCCCTTTAGACAACTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG