Sequence
atgc intronic sequence ATGC exonic sequence...tcatttatagtactatgttgacccatattgggttcaaacctttctcctgccttaggcagttagcatgaaatgcactttctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 6
tcatttatagtacta-tgttgacccatattgggttcaaacctttctcctgccttaggcagttagcatgaaatgc---actt---tctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
| || || | ||||| |||| || |||| || || || | ||| || |||||||| | || ||||||||||| |||||||||||| | ||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| ||||||||||
---gctctaatataagtgttg---tgtattcagtacaaaa-ttcctgctttacattgttgtttgcttgaaatgcttaatttgaatctgaagtgaaatgctgctgcagGAATTGTATCAAAGGGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGCGAGTGTGGTGGAAAGATGCATATGGCTGAGA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 6
tcatttatagtactatgttgacccatattgggttcaaacctttctcctgccttaggcagttagcatgaaatgc---actt---tctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
| || | | | | |||| || |||| | | | | | ||| || |||||||| | || ||||||||||| |||||||||||| | ||| || ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||
-----tttatttatttagtattgtgtattcagtgcaaaaaccctgctttacattgttggtt-gcttgaaatgcttaatttgaatctgaagtgaattgctgctgcagGAATTGTATCAAAGGGCTCTTTCCATCAAATCGGCGATACCACATCCAAGAATCATGGGTATAATTCGTGAGTGTGGTGGGAAGATGCATATGGCTGAGA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G17660.3 (Glycine max), 3'ss of exon 6
-----tcatttatagtactatgttgacccatattgggttcaaacctttctcctgccttaggcagttagcatgaaatgcactttctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
| |||| | | | | | || | | | |||| || || ||| | | | | | | | | | | | ||||| |||| || ||||| || | || || ||||| || || |||||||| || ||||| ||||| | |||||||||||| || ||||| |||||||||
ccttttaattttttttcccgtacatagacaccccttatgtagag---tctcatgtaaaagtttgtttactggtatttatcagtgtccatt--atattaaatgcagCAACTTTACCAGAAAGCACTCACTATTAAGTCAGCAATTCCCCATCCAAGGATAATGGGAATAATCCATGAATGTGGTGGGAAAATGCATATGGCTGAGC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------tcatttatagtactatgttgacccatattgg--gttcaaacctttctcctgccttaggcagttagcatgaaatgcactttctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
| ||| | | | | | || || | | | |||||| ||| ||| | | | || || ||| | || | ||||| ||||||| || || ||| ||||||| || || ||||||||||| || |||||||||||||| || || ||||||||||| ||||||||||| ||
gtaaatgtcataagctacatggtttcttacaattttgagattctgcaattttattgctgcatactttcttctggcttttgtgactgagactcaaca-acactcttgaatgga-------tgcagCAACTATACCATAAGGCACTTGCCATCAAGTCTGCCATACCTCATCCTAGGATCATGGGTATAATCCGCGAGTGTGGTGGAAAAATGCACATGGCAGAAC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 6
--tcatttatagt-actatgttgacccatattgggttcaaacctttctcctgccttaggcagttagcatgaaatgcactttctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
| | | ||| | | | | ||| ||| | | | | | | ||| | | | | ||| | | | || | | |||||| ||||||| ||||| ||| | ||||||||||| ||||| ||||||||||| ||||| ||||||| |||||||||||| || ||||| ||||| |||
atttttctggagtcataacttccatacat-ttgcctgctattttgtatgctgtatcaattgtattgactgagttttatccaactacatgga--ttaactgcagCAACTATACCAGAAAGCACTTACAATCAAATCAGCCATACCCCATCCAAGAATAATGGGGATAATTCATGAATGTGGTGGGAAAATGCATATGGCAGAGC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 6
tcatttatagtactatgttgacccatattgggttcaaacctttctcctgccttaggcagttagcatgaaatgcactttctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
| || | |||||| | | ||| | || || |||||||| || ||| |||| ||| ||||||| | || |||||||| ||||| ||||||||| | |||||||| || || | || || || ||||||||||| ||||||||||
----------------------------------------------gtatct-atgcagtt--ctttttatg-atattttgc--tgaacctcggcctcagCAACTCTATCAAAAAGCTTTGTCTATCAAATCGGCGATTCCTCATCCACGCATCATGGGAATCATCCACGAGTGCGGCGGAAAGATGCATATGGCTGAGA
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 6
tcatttatagtactatgttgacccatattgggttcaaacctttctcctgccttaggcagttagcatgaaatgcactttctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
| || | |||||| | | | |||| | |||||||| || ||| |||| ||| ||||||| | || |||||||| ||||| ||||||||| | |||||||| || || | || || || ||||||||||| ||||||||||
----------------------------------------------gtatct-atgcagttttttttatg---atattct--actgaacctcggcctcagCAACTCTATCAAAAAGCTTTGTCTATCAAATCGGCGATTCCTCATCCACGCATCATGGGAATCATCCACGAGTGCGGCGGAAAGATGCATATGGCTGAGAMapped 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|55827482|gb|AU032236.2|AU032236EST: CTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAG GAACTATATACANAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGA
genomic: CTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacata ... tctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgccttaggcagttagcatgaaatgcactttctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
cctctgct CT-rich tract
atgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatttatagtactatgttgacccatattgggttcaaacctttctcctgccttaggcagttagcatgaaatgcactttctgaagtgaacctctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGAATCATGGGTATAATTCGTGAATGTGGTGGAAAGATGCACATGGCTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcactt