Sequence
atgc intronic sequence ATGC exonic sequenceAGGTTTTGCTCAGTATGTGCCAAATGACAATCTTTTGATGACTAAAGAGCAGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgtacacaacattttctaacttatcagtagagtttattcttaagcaaatgacttaattatgtgattttttttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62500.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA12G06580.1 (Glycine max), 5'ss of exon 4
AGGTTTTGCTCAGTATGTGCCAAATGACAATCTTTTGATGACTAAAGAGCAGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgta-------cacaacattttctaacttatcagtagagtttattcttaagcaaatgactta-attatgtgattttttttcag------------------
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TGGATTTGCCCAATATGTTCCCAATGAGAACCTTTTCATGACAAAGGAGCAGCTTTTTGATATCACTTGTATGACACTTGGTGGTCGGGCTGCTGAGCAGgtagttttgacatttcctttttttttttttttttacctttctctctcctgtttttcttctatattctctgctgtatggctagatctttctgttgaaagaa
upper sequence: LOC_Os01g62500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA12G06530.1 (Glycine max), 5'ss of exon 7
AGGTTTTGCTCAGTATGTGCCAAATGACAATCTTTTGATGACTAAAGAGCAGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgta--cacaacattttctaacttatcagtagagtttattcttaagcaaatgactta---attatgtgattttttttcag---------------------
|| ||||| || ||||| || ||||| || ||| | ||||| || |||||||||||||| ||||| || |||||||| || || || ||||||||| ||||| |||||| || || | || | || ||| | ||| ||| | || | | | | |
TGGGTTTGCCCAATATGTTCCCAATGAGAACCTTCTCATGACAAAGGAGCAGCTTTTTGATATGACTTGTATGACACTTGGCGGTCGGGCTGCTGAGCAGgtagttttgacatttccttttttttttgtttacctttctctctcctgtttttcttctatattctttgctgtatgtatggctagatctttctgttgaaaga
upper sequence: LOC_Os01g62500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G29080.1 (Arabidopsis thaliana), 5'ss of exon 7
AGGTTTTGCTCAGTATGTGCCAAATGACAATCTTTTGATGACTAAAGAGCAGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgtacacaacattttctaact--tatcagtagagtttattcttaagcaaatgacttaattatgtgattttttttcag-------------------------------
|| ||||| || || || ||||| || || ||| | ||||| |||||||| || ||||||||||| |||||||| || || ||||| || |||||| ||||| | | |||| | || | | |||| || | || | | ||| |||| || || |
CGGATTTGCACAATACGTTCCAAACGAAAACCTTCTCATGACCAAAGAGCAACTCTTTGACATGACTTGCATGACTCTCGGAGGCCGTGCAGCTGAGCAGgta-----aaatccctaattgctactaatgtgaattatcctcga-cagaaaatataagaatgttgttgttcaagatgttttaagtttctggtcctatctcaacgtag
upper sequence: LOC_Os01g62500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 5'ss of exon 7
AGGTTTTGCTCAGTATGTGCCAAATGACAATCTTTTGATGACTAAAGAGCAGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgtacacaacattttctaa--cttatca---------gtagagtttattcttaag-caaatgacttaattatgtgattttt----tttcag----------
|||||||| |||||||| || ||||| || ||| | ||||| || ||||||||||| |||||||| || ||||| || ||||| ||||| ||||| ||||| || |||| | | ||| ||| |||| || || | || | | | ||| |||| ||| | | |
TGGTTTTGCCCAGTATGTTCCTAATGAAAACCTTCTCATGACCAAGGAGCAGCTTTTCGACATGACATGTATGACCCTTGGTGGTCGAGCAGCTGAACAGgtagctaatatttctttagtcttttcatattgttgggtaggattaatgttaaaaatgcacaaagaagctatctgatgtttgtaactcctgaaatcagcct
upper sequence: LOC_Os01g62500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S346_22V6.1 (Physcomitrella patens), 5'ss of exon 8
AGGTTTTGCTCAGTATGTGCCAAATGACAATCTTTTGATGACTAAAGAGCAGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgtacacaacat--tttctaacttatcagtagagtttat--tcttaagcaaatgacttaattatgtg-attttttttcag-----------------------------------------------------------------------------------------------------------------------
|||||||||||||||| | |||||||| ||||| | ||||| || ||||||||||| |||||||| || |||||||| || || || || |||||| ||||| | || | ||| | | | | | || |||| | | ||| ||||| | || | || || ||
AGGTTTTGCTCAGTATTTACCAAATGAGAATCTGCTTATGACAAAGGAGCAGCTTTTGGACATGACATGTATGACACTTGGAGGTCGTGCCGCTGAGCAGgtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatg-cttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagMapped 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|58606880|gb|CK034913.1|CK034913EST: AGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAG GTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTT
genomic: AGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgtacacaaca ... tttttttcagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGGTTTTGCTCAGTATGTGCCAAATGACAATCTTTTGATGACTAAAGAGCAGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgtacacaacattttctaacttatcagtagagtttattcttaagcaaatgacttaattatgtgattttttttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG