Sequence
atgc intronic sequence ATGC exonic sequence...tgtgataaacatagaacatcttattacaaaaaaaatactctgtcaaggacaaaaaagaaccttctgcgattataagtattttttttgttaataatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g49420.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 12
-----------------------------------------------------------------------------------------------tgtgataaacatagaacatcttattacaaaaaaaatactctgtcaaggacaaaaaagaaccttctgcgat-tataagtattttttttgttaataatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
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gtaagtgagatgatgaaccattggatttggtgcattttctttgcttgttagggttgtgacttgtgagcactgaacaatacatcacaatttgatgtcactctagatttattacctctgaacatgaaacataaatgcactattgaatattggtaaactaaacaccatatgtacatttttaactttccaccaat-ttagGGTAAGAATAAATCACCAGAAGAAAGAAGGATTGCCATATGCATTTTTGATGATGTTGCTGAGCATTGCCGTGAAGCAGCAGTTAG
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 13
-----tgtgataaacatag-aacatcttattacaaaaaaaatactctgtcaaggacaaaaaagaaccttctgcgattataagtattttttttgttaataatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
| ||| || | | | | | | || || | | | |||| | | | | || | | ||| || | || | ||| |||| | |||||| || || || |||| ||||| || || ||||||||||||||||||||||| ||||| ||||| ||| | |
acgtatcagatgcactttttggctttctgatgtggtaccaa-acacaacctaagacatgtaggtcattattttgactcttagt-ttaatgttttggata----tagGGAAGGGACAAGACTCCTGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTATTAA
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G28950.1 (Glycine max), 3'ss of exon 15
tgtgataaacatagaacat-cttattacaaaaaaaatactctgtcaaggacaaaaaagaaccttctgcgattataagtattttttttgttaat---aatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
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---ttcacgtatcagatacactttttggctctctgatgttgtaccaaacacaactaaaacatgtacgtcattgttttgacttagtttaatgttttggatat-agGGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAA
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 13
------tgtgataaacatagaacatcttattacaaaaaaaatactctgtcaaggacaaaaaag-aaccttctgcgattataagtattttttttgttaataatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
| | | || ||| | ||| ||| |||| | | || | | |||| | || || | | | || | | ||| | || ||||||| || || |||||||||| |||||||||||||||||||| ||||| || || || ||||| || | |
tctggttcaggtgaatgtagtttctaa-attctgtggctgttaccatgtctctggtacaatattagtcttcgttcaccttatgtgtat------tcgatgaattcagGGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAA
upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 13
-tgtgataaacatagaacatcttattacaaaaaaaatactctgtcaaggacaaaaaagaacctt--ctgcgattataagtattttttttgttaataatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
| | | | | || || ||| | | ||| | | ||| | ||| || | || | | ||||| | | | ||| ||| || ||||||| || || |||||||||| || ||||| |||||||||||||||||||| ||||| ||||| ||| | |
ccattttttgctgtgtattgttttttccaatt---tttcaatgttgaattctgtgaagcagcttgacttgcagcatcattcatttttaaatgattttatccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggacaaaaaagaaccttctgcgattataagtattttttttgttaataatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
tgttaat putative branch site (score: 3)
tgcgattataagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgataaacatagaacatcttattacaaaaaaaatactctgtcaaggacaaaaaagaaccttctgcgattataagtattttttttgttaataatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG