Sequence
atgc intronic sequence ATGC exonic sequenceGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctag
Basic information
species | Oryza sativa |
transcript | LOC_Os02g03260.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G370852_T03 (Zea mays), 5'ss of exon 5
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccagtgaatgtgcta-atgcaggaatctggtggtttcata-------ggacaggattaacctgctccaattgttgtctag
|| |||||||||||||||||||| |||||| |||| |||||||| || || || ||| ||||||||||||||| | ||| | | | | | |||| | ||| || | | || || | ||| || ||||||||| | |||||
GCTAATCCAGACTACAAGGGTGTCTGCCACATTGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAGgtacctt-gctgagttttccatgtacaggtcacctgtgattgtagaacatgttgggaagcactaatcttctccaattgctatctag
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccagtgaa--------tgtgctaatgcaggaatctggtggt--ttcataggacaggattaacctgctccaattgttgtctag--------------
| |||||||||||| |||||||||||||| |||||||||||||| || |||||||| || ||||| ||||| ||| | | | || | || | || | || | ||||| | | | | | ||| | |
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G34160.1 (Glycine max), 5'ss of exon 5
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgta--cttccagtgaatgtgctaatgcagg----aatctggtggtttcataggacaggattaacctgctccaattgttgtctag
|| |||||||| || || |||||||| ||||||||||| || || || |||||||||||||| || |||||| ||| | | ||||| || | ||| || | || || | ||| || | ||| | |||
GCTAATCCAGATTATAAAGGTGTTTGTCACGTTGCTCTAGCACAGGAAGGTCATTGCAGACCTGGAGAGgtaagtttctgttaacaaagctaagacatgttaaaatttgaaatctacaggtttcaaagatgttctgatc-acttgataa-tag
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 5
-GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgt--actt-------ccagtgaatgtgctaatgcaggaatctggtggt--ttcataggacagga--ttaa--cctgct---ccaattgttgtctag--------
| |||||||||||| |||||||||||||| ||||| |||||||| || |||||||| || || || ||||| ||| ||||| | | || | || | | || | || | ||||| | || |||||| | |||| | |||
GGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGAggttcgcttagtttaaccagtttttattttattatagtgaagtattgttcatttgtttgacagaagtttggttcctgctttgctaatttctctctgttacctgca
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 5
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgta-------cttccagtgaatgtgctaatgcaggaatctggtggtttcata-ggacaggattaacc-tgctccaattgttgtctag------------
|| ||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| ||||| |||||| ||| || || || || | | ||| ||| || ||| ||| | || | || || || || ||| |
GCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAGgtaaagatctctttcactggatatgat----tggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatag
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 5
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtac--ttccagtg--------------aatgtgct-aatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctag
| || ||||| || || ||||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| | ||| || ||| || | ||| |||| | |||| | || | | ||||| | || || | |
GTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAGgtgcatttctcttgccaaatcattttttaatctgttcaattttttaatcctttatattcacaatacttgttgaacct-ttacactttctcacag-
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 5
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtac--ttccagtga-atgtgctaatgcagga---atctggtggtttcatagg---acaggattaacctgctccaattgttgtctag----------
|| ||||| || ||||| ||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||||| ||| || | || || | || | || | ||| ||| | | | ||| | | | ||
GCCAATCCGGATTACAAAGGTGTATGCCATGTTGCCCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAGgtacatttctcttgccaagtcctttttcaaaatctatttaaactttttatatctttatatgcacaacacttgttgaaccctatatacattctcacag
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ32611 (Selaginella moellendorffii), 5'ss of exon 4
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctag
|| ||||| |||||||||||||||||||||||||||||||||||||| ||||| ||| | || |||||||| || | || ||| ||| || || | | || | | || | || | |
GCGAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAGgtgagtctgatatttg-----atg------tcttgta-ttgcgtgagagacggttcagttgttgtctctag-------
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ16666 (Selaginella moellendorffii), 5'ss of exon 4
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctag
|||||||| |||||||||||||||||||||||||||||||||||||| ||||| ||| | || |||||||| || | | ||| ||| || || | | || | | || | || | |
GCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAGgtgagtctgat-----ctttgatg------tcttgta-ttgcgtgagagatggttcagttgttgtctctag-------
upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ16664 (Selaginella moellendorffii), 5'ss of exon 2
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctag
|||||||| ||||||||||||||||||||||||||||||||||| || ||||| ||||| || |||||||| || | | ||| ||| || || | | || | | || | || | |
GCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAGGAAGGTCACTGCAGTCCGGGCGAGgtgagtctgat-----ctttgatg------tcttgta-ttgcgtgagagacggttcagttgttgtctctag-------Mapped 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|29628818|gb|CB633829.1|CB633829EST: GTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG GTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAA
genomic: GTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccag ... tgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccagtgaatgtgctaatgcaggaatctggtggtttcataggacaggattaacctgctccaattgttgtctag
- - - - - - - - - - - - - - - - - - - - - AAGAGG