Sequence
atgc intronic sequence ATGC exonic sequence...tttttagcatacttattcatctgatcaaatggtatttttaattaactgtattggtaatttttttagtgggatttatcttaacatataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g16290.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G111014_T01 (Zea mays), 3'ss of exon 11
--tttttagcatacttattcatctgatcaaatggtatttttaattaactgtattggtaatttttttagtgggatttatcttaacatataa--tgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
| | || | | | | || | | ||| | | |||| | || | | | || | | | || | |||| ||| |||||||| ||||||| |||||||||||||||||||||||| |||||||| ||||| ||| ||||||||||||||| |||||||||||| || |||||||||
cataagtgaatgttttgcttaagtctttgaagtgcacctttgaatc-ctgtttatccaaccaat---gaaaaacataattaactagatcagttgctctttgtagGATAAGGATATTACCTTGAGTGGGGAGCATGTAAGAGAAGGAATGACATGCATCATTTCAGTGAAGGTCCCTAGTCCAGAGTTTGAGGGTCAAACAAAG
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 11
tttt----tagcatacttattcatctgatcaaatggtatt-tttaattaact-gtattggtaatttttttagtgggatttatcttaacatataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
|| | ||||| | | | | || | ||| | ||| ||| || | | | | ||| |||| | | | | || |||| ||| |||| || ||||||| | ||||| |||||||| |||||||| | || || || | |||| |||||||| ||||| ||||||||||| |||||||||
ttgtaaaatagcaaatgcctccctttgtttaaaatggattgttttatgagttcacaaagtggattcttttcat------tgttaaatagcattctgctctttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA19G31030.1 (Glycine max), 3'ss of exon 11
-tttttagcatacttattcatctgatcaaatggtatttttaattaactgtattggtaatttttttagtgggatttatcttaacatataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
| ||||| | | | | | || ||| | ||| || | | | | || | || | ||| | | || || | ||| |||| || ||||||| | ||||| |||||||| |||||||| | || || || | |||| |||||||| ||||| ||||||||||| |||||||||
tataatagcaaatgtctccctttgtctaaaatggattattttatgaatagttcacaaagtggattcttttcatt-gttaaatagcattctgttctttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G04130.2 (Arabidopsis thaliana), 3'ss of exon 11
tttttagcatactt-attcat---ctgatcaaatggtatttttaattaactgtattggtaatttttttagtgggatttatcttaacatataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
| | | | ||| |||||| | | |||| ||| || || | | | || | | ||| || | ||||| || | || |||| |||| |||||||||||||| |||||||| ||||| ||||||||| ||||||| || | |||| ||||| |||||||| ||||||||||| |||||||||
-gtaaaacgttcttgattcataccttcaataaataatatacttccttcatt-tcttttttgtatttataattat-tttatatttttgttggctgtgtttt-cagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G10270.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------------------tttttagcatacttattcatctgatcaaatggtatttttaattaactgtattggtaatttttttagt--gggatttatcttaacata--taatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
| | || | || || | || || | |||| | | | |||| || || || || | || |||| | | | | ||| |||| || ||||||||||| |||||||| ||||| || || ||| ||||||||||| | |||| ||||| || || || ||||||||||| |||||||||
gtactaccatgattgaactgtgaaacatgccagttatagaggttgttttttgcttacatttaa--gcatttatcttgacctgttctgaaaaggttgctaactcatagtgtaacttattgttgttggttatgttttcagGAAAAGGATATTAGCTTAAGTGGGGAACATGTTAGGGAAGGATTGACCTGCATTGTCTCAGTCAAGGTTCCGAACCCTGAGTTTGAAGGTCAAACAAAG
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S517_8V6.1 (Physcomitrella patens), 3'ss of exon 11
tttttagcatacttattcatctgatcaaatggtatttttaattaactgtattggtaatttttttagtgggatttatcttaac------atataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
||| || ||| || | | |||||| || || | | | | | | | | || || | | || | || | | |||| || ||| | || || || || | || || || |||| || || || |||||||||| ||||||||||||||||| || ||||| |||
------gcaatagtaagcataggaaacagtttggtttttatgaaaaggttattgaagccatctgaaagaggttgtactaagctggatgattttgtgggtacttcagGAGAAGGATGAAAATTTATCAGGAGACCACGCTAGGGAAGGTCTGACTTGTGTTGTTTCAGTGAAGGTTCCTAATCCAGAGTTTGAGGGACAAACTAAGMapped 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|33677997|gb|CF306236.1|CF306236EST: CATTGACAAGAACAATCAATAACTTCGCAAAGAAGTCGAAGACTCTTAAG GATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGC
genomic: CATTGACAAGAACAATCAATAACTTCGCAAAGAAGTCGAAGACTCTTAAGgtgataagtt ... ctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGC
EST:
gi|58688095|gb|CK076782.1|CK076782EST: CATTGACAAGAACAATCAATAACTTCGCAAAGAAGTCGAAGACTCTTAAG GATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGC
genomic: CATTGACAAGAACAATCAATAACTTCGCAAAGAAGTCGAAGACTCTTAAGgtgataagtt ... ctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGC
EST:
gi|58686794|gb|CK075481.1|CK075481EST: CATTGACAAGAACAATCAATAACTTCGCAAAGAAGTCGAAGACTCTTAAG GATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGC
genomic: CATTGACAAGAACAATCAATAACTTCGCAAAGAAGTCGAAGACTCTTAAGgtgataagtt ... ctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGC
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:
74 (upstream exon),
45 (downstream exon)
Score:
18CAGTATCCGTACTATTGATGGTGGTACTCATATTGATGGGCTGAAGACTTCATTGACAAGAACAATCAATAACTTCGCAAAGAAGTCGAAGACTCTTAAGgtgataagtt ... ctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtattggtaatttttttagtgggatttatcttaacatataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
tcttaac putative branch site (score: 18)
tgcttttt putative PPT
atttatcttaacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttagcatacttattcatctgatcaaatggtatttttaattaactgtattggtaatttttttagtgggatttatcttaacatataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - -agcatac
- - - - - - - - - - - gatcaaa
- - - - - - - - - - - - - - - - - - - - - - - tgtattg