Sequence
atgc intronic sequence ATGC exonic sequence...tattcaatttcaattactgtttcttcatccctaatttttctagaacaaagcgccagtacattgaacttctatttttctacctgtactttctattgtgcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGAATGCCGGAACATGAAACTGCTGCTTAAACAGCAACAAAGG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os06g16390.1 |
| intron # | 12 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g16390.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G157820_T02 (Zea mays), 3'ss of exon 12
------tattcaatttcaattactgtttcttcatccctaatttttctagaacaaagcgccagtacattgaacttctatttttctacctgtactttctattgtgcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGAATGCCGGAACATGAAACTGCTGCTTAAACAGCAACAAAGG
| | | |||| | ||| | || | || ||||||||||| ||| | ||||||| |||||| | || | || | || ||| | |||||||| |||||||||||||||||||| || ||||| ||||| |||||||||||||||||||||||||||||||| |||||||| |||||||||
agcttgaactaattttctagagctggt--ttaaatccatttttttctagaataaatcatcagtacactgaactacaat----ccacttatatttttcaacttgcagGTGTGGTGATGGTACATTGGGAGTTCCAAACCAGAGAGGAGATAATTATGAATGCCGGAACATGAAACTGCTTCTTAAACAACAACAAAGG
upper sequence: LOC_Os06g16390.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA01G39490.1 (Glycine max), 3'ss of exon 14
---tattcaatttcaattactgtttcttcatccctaatttttctagaacaaagcgccagtacattgaacttctatttttctacctgtactttctattgtgcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGAATGCCGGAACATGAAACTGCTGCTTAAACAGCAACAAAGG
| | | | | || | | | | | | | |||| ||| | | || | | || |||||||| || || | | ||||| || || ||||||||| | || | |||| ||||||||| |||||||||||||| | |||||||| || || || |||||||| ||||||
aagtgcttataatatactattcctgttatgttgattactagtctatctcaa-gtctctgtttgctatgatact-tttttctatttgggtcttat-tgttgcagTTGTGGCGATGGTACACTAGGGATTCCTAGCCAAAGAGGGGATAATTATGAATGTAGAAACATGAAGCTTCTTCTCAAACAGCAGCAAAGG
upper sequence: LOC_Os06g16390.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G23380.1 (Arabidopsis thaliana), 3'ss of exon 12
tattcaatttcaattactgtttct--tcatccctaatttttctagaacaaagcgc-cagtacattgaacttctatttt------------tctacctgtact-------------ttctattgtgcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGAATGCCGGAACATGAAACTGCTGCTTAAACAGCAACAAAGG
|| | ||| | | | || ||||||| | | | ||| || || | || ||||| | |||| | || | |||| || | |||| || | || |||||| | | || ||||| | ||||||||| ||||||||||| ||| |||| |||||| |||| || ||||| |||||||||
---gtaagtcttattggggatgcaaatccatcctaattggtttcttagaaaatgctcaagaaatgcaactttttttttagtagttccagatgcacttatactgtgtctgaatgaatttgaatgtgtagTGGTGGGGATGGTTCGCTTGGGGTCCCAAGCCAAAGAGGCGATAATTATGAGTGCAGGAATATGAAATTGCTCCTGAAACAACAACAAAGG
upper sequence: LOC_Os06g16390.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 10
tattcaatttcaattactgtttcttcatccctaattttt-ctagaacaaagcgccagtacattgaacttctatttttctacctgtactttctattgt-gcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGAATGCCGGAACATGAAACTGCTGCTTAAACAGCAACAAAGG
| || | || || ||||| | || || ||| | | || ||||| | | ||| || || |||| || ||||||||||| | || || || | |||||||||||||||||||||||| | || ||||| || || || |||||||||||||||
--tccattctctcgctctctttctcaactatatgttgttgctactctgattttctcactgtacaaatttctaccatctgagctgcttgaactggcgttgcagTTGTGGTGATGGTACTCTTGGTGTACCAAGCCAAAGAGGTGATAATTATGAATGTAGAAATATGAAGCTTCTTCTCAAACAGCAACAAAGGMapped 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|58668220|gb|CK056906.1|CK056906EST: GCTGCTGACAGGGAATGTGATCCTGATGTGTGTAGAAACTGCTGGGTAGG GTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGA
genomic: GCTGCTGACAGGGAATGTGATCCTGATGTGTGTAGAAACTGCTGGGTAGGgtatgtattt ... tattgtgcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGA
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:
70 (upstream exon),
71 (downstream exon)
Score:
16GTTGCCATTGCGCAAAGAGTCAGTGTCGCAGCCGGCAGTGTCCATGCTTTGCTGCTGACAGGGAATGTGATCCTGATGTGTGTAGAAACTGCTGGGTAGGgtatgtattt ... tattgtgcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGAATGCCGGAACATGAAACTGCTGCTTAAACAGCAACAAAGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaagcgccagtacattgaacttctatttttctacctgtactttctattgtgcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGAATGCCGGAACATGAAACTGCTGCTTAAACAGCAACAAAGG
ctttctatt CT-rich tract
ttctattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattcaatttcaattactgtttcttcatccctaatttttctagaacaaagcgccagtacattgaacttctatttttctacctgtactttctattgtgcagGTGCGGTGATGGTACATTGGGAGTCCCTAACCAAAGAGGTGATAATTATGAATGCCGGAACATGAAACTGCTGCTTAAACAGCAACAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - tactgtt
- - - - - - - - - - - -ttcatcc
- - - - - - - - - - - - - - - - - - - - - gaacaaa
