Sequence
atgc intronic sequence ATGC exonic sequence...catcagtacaagcgttgaaagtagaaaattgtacctggctattagatggacataaacattcctgagattaattactgacacagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56670.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 6
catcagtacaagcgttgaaagtagaaaattgtacctggctattagatggacataaaca-ttcctgagattaattactgaca--cagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
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-aacatcaccc-tgtcaatctcacctagtttccattcgtgctcaaatgggcataagcagtttttgagtttgactgctgagagctgacactatattattc-cagATAACATCAACGGCTGGTGGTGGTACTTTGACACTGGAATTTGGCATATTGAGTCGCTTGACTAATAATACTG
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 5
catcagtacaagcgttgaaagtag----aaaattgtacctggctattagatggacataaacattcctgagattaat----tactgaca--cagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
| | ||| | || | |||| || ||| | || || ||| | || || | | | | || | ||| || | ||||||||||||||||||||||||| || ||||| || |||||||| || || || || ||||| ||||||
-------atattttctgagatcagttctgatcttgt-tttgtttatcatatttcttcaactattttttgtgtttatattgtgttaaaagttagtacttttgtgct--tagATAACTTCAACAGCTGGTGGTGGGACCTTGACTCTTGAATTTGGAGTTCTAAGCCGATTGACAAATGATCCTA
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 7
catcagtacaagcgttgaaagtagaaaattgtacctggctattagatggacataaacattcctgagattaattactgac-acagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
| |||| ||| |||| |||| | | |||||||||||||||| |||||||| |||||||| |||||||||| || || || || || ||||||||| |
------------------------------------------------------------gttcagatacatttctgattgtctgatttgtctttttttagATAACTTCAACAGCAGGTGGTGGGACTTTGACCTTGGAATTTGGGGTGCTTAGCCGCTTAACTAATGATCCCAMapped 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|29678673|gb|CB674948.1|CB674948EST: CATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAG ATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTG
genomic: CATTTGGATCAGTAAATTTATTGTATGGAGTCGATGAAAATGAAAGCAAGgcaagcttat ... gtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggacataaacattcctgagattaattactgacacagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
tactgac putative branch site (score: 1)
attttagtaataaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catcagtacaagcgttgaaagtagaaaattgtacctggctattagatggacataaacattcctgagattaattactgacacagcattttagtaataacagATAACTTCAACAGCTGGTGGTGGCACTTTGACACTGGAATTTGGTGTCCTGAGTCGTTTGACTAATGATAGCG
- - - - - - - - - - gtagaaaa
- - - - - - - - - - - - - - - gtacctg
- - - - - - - - - - - - - - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactga