Sequence
atgc intronic sequence ATGC exonic sequence...aacaacttatagtaatgcagatttgctgtttcgtggatgatatcatggttagggtgattagcacacttttttgcctaaaaaggtgaacttgtattgacagGTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAATCTCTTCCAGTCATTAGGAAACACATTTGCCAACACTATCTGGGAAGATA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g33600.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 15
------------aacaacttatagtaatgcagatttgctgtttcgtggatgatatcatggttagggtgattagcacacttttttgcctaaaaaggtgaacttgtattgacagGTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAATCTCTTCCAGTCATTAGGAAACACATTTGCCAACACTATCTGGGAAGATA
| || |||| || ||| | || | | | ||| |||| |||| | ||| || | | |||||||| ||||||||||| ||||| |||||||||||||| ||||||| |||||||||||||||||| |||||| |||| ||||| |||||||| || |||||||||| |
ccaagcaggcactgtaggttgcagtagtgactattatagctctcttctgtaa-atcgccgttaatgtgaccaatgaact-----------gaaattcacattgtattggcagGTAAGATCCCTGACGCTTGATGTCAGGGTTTGGGAGCAATCTGTAATCAATCTCTTTCAGTCAATAGGCAACACTTTTGCCAATTCTGTCTGGGAAGAAA
upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 16
---aacaacttatagtaatgcagatttgctgtttcgtggatgatatcatggttagggtgattagcacacttttttgcctaaaaaggtgaacttgtattgacagGTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAATCTCTTCCAGTCATTAGGAAACACATTTGCCAACACTATCTGGGAAGATA
| | || ||||||| ||| | || | || || | | | ||||||| |||| || ||| | | ||| |||||||||||||||||||||||||| | || ||||| || ||||| | | | | | ||||| | || || ||||| ||| | | ||||| ||
cagtatcatttttagtaatttt--tttatcagtaaaagggaaaacaaatccttttgttttcattctcacttttgcagctaagttgggaaacattttttg-cagGTAAGATCACTGACACTTGATGTTAAAGTGTGGGATCCCTCTGTTTTAAGTATGCTTAAGTCACTGGGCAATCTTTTTGCAAACTCAGTTTGGGAGGAGC
upper sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ08060 (Selaginella moellendorffii), 3'ss of exon 15
aacaacttatagtaatgcagatttgctgtttcgtggatgatatcatggttagggtgattagcacacttttttgcctaaaaaggtgaacttgtattgacagGTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAATCTCTTCCAGTCATTAGGAAACACATTTGCCAACACTATCTGGGAAGATA
| || | || || | |||||| | || | |||| || ||||| | || ||||||||||||||| |||| ||||||||||| ||||| | || || || | |||||| | || ||||| | || ||||||||
--------------------------------------------gtacttggcgttgata-taaacttttgtctct-------tatgtttgtcgtg-cagGTGCGTTCCCTGACACTTGATGTCCGGGTGTGGGAGCCATCAGTAATTGGATTGTTTCAATCTATTGGAAACGCCTTCGCCAATTCAATGTGGGAAGAACMapped 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|58667459|gb|CK056145.1|CK056145EST: GCATCGAATGCTCTGGGGTACACAGAAATCTCGGTGTGCATATATCTAAG GTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAAT
genomic: GCATCGAATGCTCTGGGGTACACAGAAATCTCGGTGTGCATATATCTAAGgtaagcaagc ... gtattgacagGTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAAT
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:
63 (upstream exon),
58 (downstream exon)
Score:
14TGGTGCAGCAGAGCCTGACTGGGCATCCCTAAACCTTGGAATTCTTCTATGCATCGAATGCTCTGGGGTACACAGAAATCTCGGTGTGCATATATCTAAGgtaagcaagc ... gtattgacagGTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAATCTCTTCCAGTCATTAGGAAACACATTTGCCAACACTATCTGGGAAGATA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttagggtgattagcacacttttttgcctaaaaaggtgaacttgtattgacagGTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAATCTCTTCCAGTCATTAGGAAACACATTTGCCAACACTATCTGGGAAGATA
gcctaaa putative branch site (score: 14)
actttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacaacttatagtaatgcagatttgctgtttcgtggatgatatcatggttagggtgattagcacacttttttgcctaaaaaggtgaacttgtattgacagGTAAGATCACTGACACTTGATGTCAGGGTCTGGGAGCCATCTGTAATCAATCTCTTCCAGTCATTAGGAAACACATTTGCCAACACTATCTGGGAAGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
aacaact
- - - - - - taatgca
- - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - gtggatg
- - - - - - - - - - - - - - - - - - - - - -catggtt