Sequence
atgc intronic sequence ATGC exonic sequence...ctgcactgatacttggggatggtaattggtaagcgagaatgggatgctgcgagttgcttttactcttactgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g08400.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
ctgcactgatacttggggatggtaattggtaagcgagaatgggatgctgcgagttg---cttttactcttactgtttcttaatatatac--gcttatttcct-cagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
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-----gtaatgctcaagaaca-caccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaactaacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 4
--ctgcactgatac--ttggggatggtaattggtaagcgagaatgggatgctgcgagttgcttttactctta--ctgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
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atcaagatagaagacatttataatgtttccttttcataaattcttgaattttacttataaaacagaggctaaaactggttcttgggaaatgtgcttg------cagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 8
-ctgcactgatacttgggg-atggtaattggtaagcgagaatgggatgctgcgagttgcttttactcttactgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
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tcataaatggtgcttctcatattttttgtcattttcctgcatcagtttcatagacatcatatgaaacctcacatggatgattacacaataccatttgt--agGATCTGTGCTCGGTGCAACCTTGAAATTGGTCATGAAAGACATTTGAGGCGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGTCATGCTTGTGGT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
--ctgcactgatacttggggatggtaattggtaagcgagaatgggatgctgcgagttgcttttactcttactgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
| | | | | || | | | | ||| | || | | | | | | | ||||| || || | |||| ||||| || || || | |||||||||||||| | | | ||||||||||| |||||||||||||||||||||||||| || | |||||||
tgataaatagggcttctcatgttttatgtcattctcctgcatgtg-tgtcatggacttcgtatgagacctcacatggttaat-tacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 4
-ctgcactgatacttggggatggtaat--tggtaagcgagaatgggatgctgcgagttgcttttactcttactgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
|| | | || ||| | | | || | | | || | || | || || | | | || ||| |||| ||||| || || | | ||||||||||||||| ||||| || ||||||||||| || |||||||||||||||||||| | || || | |||
tctagttttctcattcaagattatttccctcatgaggaattttacacaatcacaaggaacattatcaaataatgccct---gtttctgtatttttttggatagGATCTGTGCTGGTTGCAATACTGAGATTGGTCATGGACGTTTTCTAAGTTGCATGGGTGCAGTTTGGCATCCAGAATGTTTCAGATGCCACGGTTGCGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgcgagttgcttttactcttactgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
tcttaat putative branch site (score: 3)
cttatttcctc putative PPT
tgtttcttaatatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgcactgatacttggggatggtaattggtaagcgagaatgggatgctgcgagttgcttttactcttactgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT