Sequence
atgc intronic sequence ATGC exonic sequenceGTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATGgtacgactgtacgatcgatattttttttccttaacaacaagagtgcatgatcataaaatggtaacatgcatgctctaatatgaacaaaactgagtccaca...
Basic information
species | Oryza sativa |
transcript | LOC_Os08g32630.3 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G851815_T02 (Zea mays), 5'ss of exon 12
GTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATGgtacgactgtacgatcgatattttttttccttaacaacaagagtgcatgatcataaaatggtaacatgcatgctctaatatgaacaaaactgagtccaca---
||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| || |||||||| |||||||| | |||| | |||| || || |||| || | | ||| | || |||| |||| | || ||| || |||||||| || ||||| ||| | |
GTTGGCGATGCTAGTGGAATACAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACGAGACATCTTGGCCGTTTGTCTAGTGgtttgtctgt-tgaattatccttttcttaatatataactgt--ttgattatcaaaaaaaaggaatatgtttgatctaatattaagaaaacagagcaaagagtg
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA14G05100.1 (Glycine max), 5'ss of exon 13
GTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATGgtacgactgtacgatcgatattttttttccttaacaacaagagtgcatgatcataaaatggtaacatgca-tgctctaatatgaacaaaactgagtccaca
|||||||||||||||| || || ||||||||||| ||||| || |||||||||||||| ||||| || || | ||||| ||||| | || | | | | || | || | | | || | | || | | |||| || | | | | | ||
TTTGGTGATGCTAGTGGCATACAATCACCTGTTTCATTTGGTGGATTTGGAAGCTTGACCAGGCACCTGGGGAGACTGTCAGCTGgtaagcct-ttcagtgaaatttcaaacttctgatgtatacttttgaactagttgaagcagatctattgcaatgttgtggaacaggaggctttttattttca
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 5'ss of exon 11
lower sequence: AT2G32640.1 (Arabidopsis thaliana), 5'ss of exon 12
GTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATGgtacg-------actgtacgatcg-atattttttttccttaacaacaagagtgcatgat-cataaaatggtaacatgcatgctctaatatgaacaaaactgagtccaca------------------------
||||||||||||| || || || ||||||||||| ||||| ||||||||||| ||||| || || ||||| | ||||| ||||||| ||| | || | | | || | || | | | ||| || || | || |||| | || | | | | | | | |||
TTTGGTGATGCTAGCGGTATTCAATCACCTGTTTCATTTGGGGGTTTTGGAAGTTTGACCAGACACCTTGGAAGATTGTCCAATGgtatatacactcactctctgagagtacacttgctgtctccatatctcattgaacattatacaactttttatatcatgaactctttcagaatattcagatttt-ctgacaatcttattgttcaacttaaaaaag
upper sequence: LOC_Os08g32630.5 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv12s0059g01150.t01 (Vitis vinifera), 5'ss of exon 12
GTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATGgtacgactgtacgatcgatattttttttccttaaca-acaagagtgcatgatcataaaatggtaacatgcatgctctaatatgaac--aaaactgagtccaca
||||||||||||| || || |||||||| ||||| ||||| |||||||| |||||||| ||||| |||| | ||||||| |||||| | | | | || || | | | || | | ||| || || | | | || ||| | || || |
TTTGGTGATGCTAGCGGCATACAGTCACCAGTTTCATTTGGTGGTTTTGGGAGCTTGACCAGGCACCTTGAGAGGTTGTCAACTGgtac-attctcaatttgaaatcggagaagcattgtatactttgttttctaatcttacaacgtcgattaattattgggagtaataactcagaattgctgtta--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|29670150|gb|CB666425.1|CB666425EST: TTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATG GTATATATGAAGCAGTTTCAGGAGATCTTCTGGATGCACGTAGTTTGCAGC
genomic: TTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATGgtacgactgt ... ggcgctaaagGTATATATGAAGCAGTTTCAGGAGATCTTCTGGATGCACGTAGTTTGCAGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGGTGATGCTAGTGGAATCCAGTCACCTGTTTCTTTTGGAGGTTTTGGAAGCTTGACAAGGCATCTTGGTCGTTTGTCAAATGgtacgactgtacgatcgatattttttttccttaacaacaagagtgcatgatcataaaatggtaacatgcatgctctaatatgaacaaaactgagtccaca
- - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - TGGAAG