Sequence
atgc intronic sequence ATGC exonic sequence...tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g05690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G129413_T01 (Zea mays), 3'ss of exon 1
tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatg-----aaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
| | | || |||| | | | || || || ||| | | || || | | | || | | || || ||| |||||||| ||||||||||||||||| || |||||||||||||| |||||||||||||||||| ||||||||||||||||||| || || || || | ||
tgccaccgacacatgggt-----cccagcctgccacgaggcaccatgactcgttgcttccgttgttgtgtgcgcttctttttgacgttgatacatacatatgtagGGAGATCATGCACGCGATGTGGCGTCCTCAGAAGTTCAAGGCCATCTACCTGCTGGCGACGCTGTACGTGCTGACGCTGACCCTCCCTTCCGCCGCCGCC
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 5
tatctataaaacttgggagtag-attgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
| |||| | || | ||| || || | | || || | | || ||| | | |||| || || | ||||||||||||||||||||||||| || || || |||||||| || ||| | ||||| || |||| ||| |||| |||| || || ||||| | ||
-aattataggagaaaagaaaaatattccttaaaagttcctggtatttttctcttaaaaacaaaaagtaaattggagaataagacgtgtgctggtgacacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTGGCTACCCTGTATGTGATGACATTGACTCTCCCATCGGCAGCTGCA
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 5
--tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
||| | |||||| | | | || || | ||| | ||| | | ||||| ||| | |||| || || ||||||||||||||||||||||||| || || || |||||||| || ||| | || || || |||| ||| |||| |||| || || ||||| | ||
aatattccttaaactttg--ctggtttttttgttgttaaaaaaataatgatattcttccaagttaattgctggagtgaataagacgtgtgttggtggcacagGGAGATAATGCACGCGATGTGGAAACCTCAAAAATTCAAGGCCATATACTTACTTGCTACCCTGTATGTGATGACATTGACTCTTCCATCGGCAGCTGCA
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaat-taagaaagtaattaagggatgaaatgcaaatgc-agGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
||| || | | || ||||| | || | || | || ||||| | | || | | | | || || | || || | |||||||||||||||||||||||| ||| || ||||||||||| | ||| | ||||| || |||| |||||||| |||||||| || ||||| | ||
gtgatatgctgctaattaattagttaattttgagagaaatgaagttggctagc--tagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatg-cagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
|| ||||| | | | | | | | | || ||| | | |||| | ||| ||||| | | | | ||||||||||||||||||||||||| ||| || ||||||||||| | ||| | ||||| || |||| |||||||| |||||||| || ||||| | ||
-atttataatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataagacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 5
tatctataaaacttgggagtagattgattttaacc--aaagtcaaaataacttatagtagtag--taattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
| |||| || |||| ||| ||||| |||| | || | | ||| ||| | ||| | | ||||| | ||||||||||||||||| |||||| ||||| |||||||||||||| || || || ||||| | || || || ||||| ||||| || || ||||| |||
--------------gtaagtattttttttttgtttggaaaaataaaatggctta-attaatggcttaactaattatgtattggaaatttgaaaaaatataatagGGAGATAATGCACGCTATGTGGAAACCGCAAAAGTTCAAGGCGATATATCTACTAGCGACCATATATGTACTAACGCTAACGCTACCATCCGCGTCTGCG
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 5
-tatctataaaacttgggagtagatt---gattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
| | | || | || | | | ||||||| | || | | || | | | ||| ||| || || | | ||| | ||||| ||||||||||| || |||||| || ||||| |||||||| || ||||||||||| || ||||| |||||||| ||||| || ||||| ||| | ||
ttttgaaaaacagtttccacttattccaaaattttaattattgtttagaaaattctaaatca-agtgtataaaaacata---aggttttgatttttttttgcagAGAGATAATGCATGCAATGTGGAAACCACAGAAATTCAAGGCCATATACCTGCTGGCTACCGTGTATGTGCTGACACTGACACTTCCGTCCGCGGCAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
aaataac putative branch site (score: 2)
tagtaattaagaaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatgcagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
- - - - - - - - - - - - - - - taaccaa
- - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaaa