Sequence
atgc intronic sequence ATGC exonic sequence...gccttctaaagggtgctggcatatctgtcataacaaggttataccattcttttacaagaatgctgacatatgataatttttgttatcattgcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAATGGATTAGAGTTCCAAAGCGCTGTGGTGATGGTGAAGAGGAACGACCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 15
gccttctaaagggtgctg-gcatatctgtcataacaaggttataccattcttttacaagaatgctgacatatgataatttttgttatcattgcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAATGGATTAGAGTTCCAAAGCGCTGTGGTGATGGTGAAGAGGAACGACCAA
| ||| | ||| | || | | | | | || | || | || | | || | ||| | | ||| ||| | |||| |||||||||||||| || |||||||| || ||| |||||||||| || ||||| | ||| | || || ||||| |||||||| ||||||||
cctgaataacagcagctttgaatttttatttttcataattttaatcaaaaagtcttgagttgtttcatgtacttctttgttttcttttatt-caatatcagGGCGGGCATTTCTCTGGCATATATAGAAAGGTTCAATTAAAGCCACTAAAGTGGATCAAAGTGGCCAAAAGCAACGGTGAAGGTGAAGAAGAACGACCTG
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 17
gccttctaaagggtgctggcata-tctgtcataacaaggttataccattctttt--acaagaatgctgacatatgataatttttgt---tatcattgcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAATGGATTAGAGTTCCAAAGCGCTGTGGTGATGGTGAAGAGGAACGACCAA
| || || || | | |||| | | || | ||| |||| || | | | | | | | | || || | | || | || | |||| || ||||||||||| || ||||| ||||| |||||||||||||| || ||| | | ||| |||| || |||||| | |||||| |||
------ttgagtgtccttttaaagcctgtaaaattgctatttttacatcttttttaaccaaagtcttaaattgtttcatttcttttccttttcttcacattatcagGGAGGACATTTCTCTGGCATCTATAGGAAAGTTCAACTAAAGCCACTAAAGTGGGTCAAAGTGACAAAAGGCAATGGTGAAGTTGAAGAACAACCTGTTG
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 13
------gccttctaaagggtgctggcatatctgtcataacaaggttataccattcttttacaagaatgctgacatatgataatttttgt---tatcattgcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAATGGATTAGAGTTCCAAAGCGCTGTGGTGATGGTGAAGAGGAACGACCAA
| | | | || | | || || || | ||| || ||||| | | | ||| | | | || || | | || | || | |||| || ||||||||||| || ||||| ||||| |||||||||||||| || ||||| | | | |||| | |||||| | |||||| |||
ttgcatgtccttttaaagcccgtaaaattgctatctttaca---------tctttttttatcaaagtcttgaattgtttcatttcttttccttttcttcacattatcagGGAGGACATTTCTCTGGCATCTATAGGAAAGTTCAACTAAAGCCACTAAAGTGGATCAAAATGACAAATGACAATGGTGAAGTTGAAGAACAACCTGTTG
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 13
--gccttctaaagggt--gctggcatatctgtcataacaaggttataccattcttttacaagaatgctgacatatgataatttttgttatcattgcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAATGGATTAGAGTTCCAAAGCGCTGTGGTGATGGTGAAGAGGAACGACCAA
|| | | | | | | |||| | |||||| || | | ||| ||| | | || | || || | | | ||| | ||||||||||||||||||| || ||||| || || ||| |||||||||| || ||||| | ||| | || || |||||| |||| ||| ||||||||
ctgcataacagcagctttggttttatatttttcataattgtaataaaaaagacttc----agacgtttcatgtactacttttgttttcttttattcaatatcagGGTGGGCATTTCTCTGGCATATATAGGAAGGTCCAATTAAAGCCACTAAAGTGGATCAAAGTGGCCAAAAGCAATGGTGAAGGTGCAGAAGAACGACCTG
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 15
gccttctaaagggtgctggcatatctgtcataacaaggttataccattcttttacaagaatgctgacatatgataatttttgttatca----ttgcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAATGGATTAGAGTTCCAAAGCGCTGTGGTGATGGTGAAGAGGAACGACCAA
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---atgtgaaaattcaaaagatcctcctcattcctttactacatcgttaagctgccctggatttgttctctttttcttgatgtcataaatgtttgctat-ccagGGGGGACATTTCTCTGGTATTTATCGGAAGGTTCAACTAAAGCCACTAAAGTGGGTTAAAGTTCCAAAAAGTAATGGTGAAGGTGAAGAAGAACGGCCTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29674285|gb|CB670560.1|CB670560EST: ATTTGGAGCATATTGAAAAGCTTCGTCAAGTCAAAGCAGTACTGGAGGAG GGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAA
genomic: ATTTGGAGCATATTGAAAAGCTTCGTCAAGTCAAAGCAGTACTGGAGGAGgtaattttta ... gcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAA
EST:
gi|29625184|gb|CB630195.1|CB630195EST: ATTTGGAGCATATTGAAAAGCTTCGTCAAGTCAAAGCAGTACTGGAGGAG GGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAA
genomic: ATTTGGAGCATATTGAAAAGCTTCGTCAAGTCAAAGCAGTACTGGAGGAGgtaattttta ... gcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcttttacaagaatgctgacatatgataatttttgttatcattgcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAATGGATTAGAGTTCCAAAGCGCTGTGGTGATGGTGAAGAGGAACGACCAA
tgctgac putative branch site (score: 2)
atatgataatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccttctaaagggtgctggcatatctgtcataacaaggttataccattcttttacaagaatgctgacatatgataatttttgttatcattgcaacactagGGTGGGCATTTCTCTGGTATTTATAGAAAAGTGCAACTAAAGCCACTGAAATGGATTAGAGTTCCAAAGCGCTGTGGTGATGGTGAAGAGGAACGACCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
gccttct
- - - - - - -tgctggc
- - - - - - - - - - - - - - cataacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgac