Sequence
atgc intronic sequence ATGC exonic sequencegtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g70200.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
--------------------------gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
| | |||| | | || | ||||| ||||| || | | | || |||||| ||||| |||| |||| |||||||| | || || || |||||||| ||||||||||||||||| || |||||||| || ||||||||||| || ||||||||||| |||||| | ||
gtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttg-gtctgatctctgatcattctgcatgttctat-agAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G000581_T01 (Zea mays), 3'ss of exon 3
--------------------------gtaaattttccgcttatctccaatacatcctatcatctgctcattggct----cgtagcatgtggagtctgatgt-------ttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
| | |||| ||| ||| | || | | | ||||| | || | | ||||||| | ||||| |||| ||| ||||||||| || || || || |||||||| ||||||||||||||||| || |||||||| || ||||||||||| || ||||||||||| |||||| | ||
gtaaatcatctatctgtctgcaagtgatgcagcttccctctatgtccgcatcttctttttccccagtcattcatcacaacactgcgtcctgggtctgatctcttatcattctgcatgttcta-cagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCGACTTACTACGAAGACATGCAGCGTTCA
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G301552_T01 (Zea mays), 3'ss of exon 10
-------------------gtaaattttcc-gcttatctccaatacatccta-----tcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
| || | | | |||| ||||| | ||| | ||||| || || || | | | || |||||| ||||| |||| ||| ||||||||| || || || || |||||||| ||||||||||||||||| || |||||||| || ||||||||||| || ||||||||||| |||||| ||
gtaaatcatctatctgtctgcaagtgatgcagcttccctccactttttcccagtcattcatcacaacactgcgtccttg-gtctgatctctgatcattctgcatgttcta-cagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCGACTTACTACGAAGACATGCAGCATTCA
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
-------gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcg-tagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
||||| | | | ||| | || || | | | || || || | || | || || || ||| ||| || || ||||||||||| |||||||| ||||||||||||||||| || |||||||| || || ||||| | ||||||||||| || |||||| | ||
gtaattaataaatcaactgtctgtctgtctgtctgtctgtctacgagtgagtgatccggcggcggcttccctcaaacgtcact-tacttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152029_T01 (Zea mays), 3'ss of exon 3
--------------------------gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
| | |||| | | || | ||||| || || || | | | || |||||| ||||| |||| ||| ||||||||| || || || || |||||||| ||||||||||||||||| || |||||||| || ||||||||| | || ||||||||||| ||| || | ||
gtaaatcatctatctgtctgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacactgcgtccttg-gtctgatctctgatcattctgcatgttcta-cagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCATCGACTTACTACGAAGACATGGAGCGTTCA
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
----gtaaattttccgc-tta------tctccaatacatcctatcatct--gctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
||| |||| | ||| | ||| || | | || | ||| | ||| || || | ||| |||| | | | ||| |||||||| | || |||| |||||||| |||||||||||||| |||||||||||||||| |||||||| | || ||||||||||| ||||||||| |
acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctct-ttgtat-agAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
||| | | | | || || || || | || ||| | | | || | ||| | || | || | ||||||||| | || | ||||||||||| || ||| |||||||||| ||||||||||| || || |||||| | || || || ||||| ||||| | ||
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttg--ggttgaat-gaatcaactcctatctaactcttttaattgattga-cagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ05285 (Selaginella moellendorffii), 3'ss of exon 3
gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
||||| || | | | | | | | || | | || | | || || || ||||| ||| | || | ||| ||||| || || | |||||||||||||||||| | || || || ||||||||||| ||||| ||||| |||||||| || || |||||| || ||
gtaaagttctc--tcaatacatagaaaagct-ttgtttg---aaaagatcttattccgt----tctgacattt---tctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTATGAGGACATGCAGCGAGCT
upper sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
||||| || | |||||||| | | | ||| | | | ||||| ||| || | ||| ||||| || || | |||||||||||||||||| | || || || ||||||||||| ||||| ||||| ||||||||||| || |||||| || ||
gtaaagttctc--------tcaatacatagaaaagctttgt--ttgaaaagatcttattcggttctgacatttgc---tgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCTMapped 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|117229672|gb|CT846639.1|CT846639EST: GGTCTGTTCTACGATACCAGCAATGATCCTGAGGGTGGATACTATGCAAG AGGTGCCCGCGCGTCGGT
genomic: GGTCTGTTCTACGATACCAGCAATGATCCTGAGGGTGGATACTATGCAAGgtaaattttc ... gtcctatcagAGGTGCCCGCGCGTCGGT
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:
50 (upstream exon),
70 (downstream exon)
Score:
18CTCATCTTATTCCCCCAGACACCCCTCGGTCTATCTTTGTATATTTCCGTGGTCTGTTCTACGATACCAGCAATGATCCTGAGGGTGGATACTATGCAAGgtaaattttc ... gtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
gtctgat putative branch site (score: 18)
tcctatc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC