Sequence
atgc intronic sequence ATGC exonic sequencegtatattgaagaaattcactagctatcattttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g59340.3 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G020002_T02 (Zea mays), 3'ss of exon 11
------------------------------gtatattgaagaaattcactagctatcattttaaacaacaa-attc--cccactattcaacgaagtacaatgat-caaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
|| || | |||| | | | |||| | ||| || ||| | | | || || |||||| | |||||||||||| ||||||| ||||||| |||||||||| |||||||||||||||||| |||||||||||||| |||||||| || |||||||| || || ||||||||||| ||||||
gtactatacattaaatctgctcaaaccagggtttagtttagaagtaaccagattgtcatatcaaaatgcattgttcaactagcaaaaaaaaaaaaaacaatggtacaaattactcaaccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATCTGACGCAGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGT
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------gtatattgaagaaattcactagctatcattttaaac-aacaaattccccactat------tcaacgaagtacaatgatcaaattactca-------aatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
| ||| | ||| | | | | ||||||| | || | ||| || | | ||| | | ||| | | |||| ||| ||||| | || ||||| ||||| || |||||||||| ||||| ||||||||||||||||||||||||||| ||||| | | ||||| || |
gtatattttctgttaatcaaagtaaaattagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaagctctttgtatagatgccaaaagtattactgatttttatttatttatttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 11
-----------gtatattgaag---aaattcact---agctatcattttaaacaacaaattccccacta------ttcaacgaagtac-aatgatcaa-attactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
|| || ||| ||||| || || | | || || || || | || || | | ||| ||| | ||| || |||| ||||||||| || || ||||| ||||| || |||||||||| |||| ||||||||||||||||||||||||||||||||| | |||||||| ||| ||
gtatatattcagttaatcaaagtgcaaattagcttctagttcttatggaaataaaaaagctttttggtaaagatgccaaaagtattactgatgttttttatttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTGTTCTCCCAGGATCTGATGCAGATATTATCATCCTGAATCCAAATTCGAGCTTTGAGATGAGT
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 11
----------------------------------------------gtatattgaagaaattcactagctatc-attttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
| ||| | |||| | | || || ||| | |||| ||| | ||| | | | | || || |||| ||||||||| || || ||||| ||||| || |||||||||| ||||| ||||||||||||||||||||||||||| ||||| | |||||||| ||| ||
gtatattttcagttaatcaaagtgaaaattatctttcagttcttatgactataaaggaaaactgtttggtaaagatgccaaaaaccaaaagtataactgtataactga-tgct----ttttgtttctacaatcatttcagTGCTAAAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTCCCAGGATCTGATGCAGATATTATCATCCTTAATCCAAATTCGAGCTTTGAGATGAGT
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 11
-------------------gtatattgaagaaattcactagctatcattttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
| | || | || | | | ||| || | || | | | | | || | | |||| ||| || || ||||||| | |||||||||||||| || ||||||||||| || || | || || ||||||||||||||||| ||||||| | |||| | || |
gtatatatgctctttcgaagcttctttttaatgttgaaaatttgctttttccaatgagcttttacttgaaagttatgtgtttgcatt--tgaaatgactttaagtttgtcagTGCTAGAATTTTCAACATATATCCACGGAAAGGAGCTATCCTTGCTGGCTCGGATGCAGATATTATCATATTGAATCCAAACTCAAGCTACGAGATTAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
tcttttc CT-rich tract
atcaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattgaagaaattcactagctatcattttaaacaacaaattccccactattcaacgaagtacaatgatcaaattactcaaatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT