Sequence
atgc intronic sequence ATGC exonic sequenceTGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g04970.1 |
intron # | 15 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 15
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattt--tgttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag--------------------------------------------------------------------------------------------------------------------------
||| ||||| ||||| |||||||| | || ||||||| | || ||||| |||||||| |||||||| |||||||||||||| |||||||||||||||||| | | ||| || ||| ||| | ||| | || | | ||| || | | || ||
TGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttcttttgctgattttcattttagatcttcca-tagcattgtttc-tggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagctttacttgcctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcag
upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 15
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag------------------------------
||| ||||| ||||| ||||| |||||||| |||||||| | || ||||| |||||||| || ||||||||||||||||| || ||||||||||| |||||| | || ||| || ||||||| | ||| ||| | | | ||| | | | |
TGGTGTTGCTCTTCTATATGCGTCAAAAGAGTTGGATAAACTTCAAACTGCTAACTTTGATCAGAAGATTGGTGTCCAGATTATCCAAAATGCTTTAAAGgttagttttctctgaattttttctgat--ttcctctttagctc-ctctaaatcgcattttgattacattacggatcttgtggaaggaaaaccagcaccagatt
upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 15
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccatttt---gttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag-------------------------
||| ||||| ||||| |||||||||| || ||||||| | || ||||| |||||||| |||||||| || ||||||||||| |||||||||||||||||| | | ||| |||||| || | || | ||| | | | || | | |||
TGGTGTTGCTCTTCTCTATGCATCAAGTGAGTTGGATAAGCTTCAAACTGCTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttcttttgctgattttcattttagattatccatagcattgtttctggtaggtcactact-ccacagatttttctctctctcatcccttatt
upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 15
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcct----ctcttgcttgctccatcta--atggctggataatgc----tgcag-----------------
||| ||||| ||||| |||||||| | ||| |||||||| | || ||||| ||||| | |||||||||||||||||||| || ||||||||||| ||||| | || ||| ||| || ||| | | | | ||| | ||| | | || || |
TGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTTAAAGgtcagttttctctgaattttttctgatttcctctttagctcctccatattgcattttttatgcttacactttgtatcttgtggaaggaaaaccagcacca
upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 13
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctct--tgcttgctc-catctaatggctggataatgctgcag--------
|| || || ||||| || ||| ||| ||| |||| ||| | | || || ||||||||||| ||||||||||||||||| ||||| || || |||||||||| | | || ||| | | || | || ||| | ||| | || ||| | | | | | |
AGGTGTGGCTCTTCTATACGCAGCAAGAGAGTTGGAAAAACTTCCAACAGCCAACTTTGACCAGAAGATTGGTGTCCAGATTATTCAGAACGCATTGAAGgttttctattc---tttagaactaaaatcctctgatctgataattgatgacaagaaattgttttaacgagttttggtttaccag
upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 14
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgct-ccatct-aatggctggataatgctgcag-----------------------------------------------------------------------------------------------------------------------------
||| || || ||| ||||||| || ||| ||||| ||| | || ||||||||||||||||| ||||| || || || ||||| ||||||||||||| ||| | || || || | | || || | | |||| ||||| | | || ||| | | |
TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtat-catttctcaacctacccgtagaagt-ccacaatgacttgtggtcatctcagttactctttaacgaagtaattcatcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagctttaaactcttctgagatgtaataaacttgtgttatagMapped 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|88224758|gb|CI224607.1|CI224607EST: CCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAG ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: CCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
EST:
gi|86493378|gb|CI136011.1|CI136011EST: CGAACTTTGACCNAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAG ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: CGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
EST:
gi|88903313|gb|CI088851.1|CI088851EST: CCAGATCATTCAAAATGCTTTGAAG ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: CCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
EST:
gi|86536911|gb|CI177117.1|CI177117EST: AAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAG ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: AAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
EST:
gi|88842319|gb|CI081575.1|CI081575EST: AGATTGGTGTCCAGATCATTCAAAATGCTTTGAAG ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: AGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
55 (upstream exon),
74 (downstream exon)
Score:
9TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG