Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g16690.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
gtaagttttgcaccttcccttg---tgagcaatgcc---tttaatatccttgttgttt-----gatcttttaacttaact-tttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
|| |||||| | |||||||||| || || | | ||||| | |||| | || || |||| | | |||||||| |||||||||| ||||| ||||| || || ||||| || ||||||||||| ||||| |||||||| ||||| || |||||||||||||||||||| ||
gtgagtttt-ctccttcccttgccttgcacaccgttcggtgccatatcatggttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 4
gtaagttttgcac----cttcccttgtgagcaatgcctt-taatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
||||||||| | ||||||||| | || | | ||||| | |||| ||| || |||| | ||||||||| |||||||||| || || ||||||||||| || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||||||||| ||
gtaagttttctgcttcccttcccttgcacaccattctatgccatatcatggttgcctgaactgttaatcca-tttttcagCTACATGGGCTGTTTCTGTGTACTTTGCATATCAACGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTATGAGATGGTTAACCACCAGGGCAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G15930.3 (Glycine max), 3'ss of exon 4
------------------------gtaagttttgcaccttcccttgtgagcaatgccttta-atatc-cttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
| | | | ||| || | | | || | | | || | || ||||||||| | | | ||| |||| ||| | |||| ||||||| ||| || || || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| || ||
gtaagcattactttcatattcgctttctctctccctcctctccctctctgtcatttgtgcatacattgcatggaatttgatcttacagatgatttttgcagCATCATTCTTTATATCTGTCTACTATGCCTATCAACGAACGTGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
-----------------------------gtaagttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
| | | | | ||| | ||| | | | | || ||||||||| | ||| ||| |||| ||| | |||| |||||| ||| || || || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| || |
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattg--catggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 4
--------------------------gtaagttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
| | | | | | ||||| | | || | | | | || ||| | | | || |||| |||||||| |||| || ||||| |||||||| || |||||||||||||| || || |||||||| ||||| |||||||||| |||||| || ||
tgttaattcttgttcttctaattacattgaagtatttgt-tagctttgtggatgtactttctgattatttcatactattataacttatttaatcattgcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
----------------gtaagttttgcaccttccc-ttgtga-gcaatgcctttaa-----tatccttgttgtttgatct--tttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
| | || | ||||| ||| | | | || || | || || |||| | |||| | | | | |||| ||||||| ||||||| |||||||| ||||| || |||||||||||||| ||||| |||||||| ||||| ||||| ||||||||||| || ||
tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaactataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
-----------------------gtaagttttgcaccttcccttg-tgagcaat-gcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
| | | || | | | | | | | || | | | ||| | | | | |||| | | | | |||| |||||||| ||||||| |||||||||||||| || |||||||||||||| ||||| |||||||| ||||| ||||| ||||||||||| || ||
gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------gtaagttttg-caccttcccttgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttca----gCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
|| ||| | | | |||| || | || | | | || | | | || || | | |||| | || |||||||| |||| || |||| ||| | ||| || || ||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||
gtaagtattagtatttacacacaaaaaactcgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G09300.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaag--ttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgat---cttttaac--ttaactttt--cagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
||||| || ||| | | | | | | |||| | || || ||| ||| || | |||| |||| | |||||| |||| || || | ||| | ||| ||||||||||| || |||||||| |||||||| ||||| |||||||||| ||| || | ||| |
gtaagaacattttccctcctttgatttcttctatgatcagtatctgtcctgcgtggctaacttgtaagaattgatttttaacagCATCGTGGGCTATATCCGTGTATTATGCTTTCCAACGTACCTGGAAACCATTCAATCCAATCCTTGGTGAGACTTATGAGATGGCTAATTACAATGGTGT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgatct-tttaacttaactttt--cagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
||||| || | ||| | | | | || | | | | || ||| ||| | | | ||| ||| |||||||| |||| || || | || |||||||||||||||||||| |||||||| || || || ||||| ||||||||| ||| || | || ||
gtaagcac-atccccactcttcttgttcttccttgtagttttttcatggtgtgactaatttcatctgatctttaatagCATCATGGGCTATATCTGTGTATTACGCCTACCAGCGTACCTGGAAGCCGTTCAATCCAATTCTCGGTGAGACTTATGAGATGACTAATCATAATGGGAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 4
----gtaagtt-ttgcaccttcccttgtgagcaatgcctttaatatcc--ttgttgtttgatcttttaacttaactttt-cagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
||| || ||||| || | || | | || |||| || || | || |||| | ||| || |||| |||||||| |||| ||||| | ||| ||||| || || ||||||||||| |||||||| ||||| ||||| ||||| |||| ||| || || ||
gtgagtatattcttgcattaaatatttcagggcatacatgtattatctggttaatggtggaactttaatgttactaattgcagCATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTTTTAATCCCATTCTTGGTGAGACTTATGAAATGGCTAATCATGGTGGAAT
upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S20_97V6.1 (Physcomitrella patens), 3'ss of exon 4
------------gtaagttttgcaccttcccttgtgagcaa-tgcc--tttaatatccttgttgtttgatcttttaacttaact----------tttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
|| | | | | |||| || || | || |||| | | || | | | || | || | | || ||||| ||||||| |||||||| ||||| ||||| ||| ||||||||||||||||||||||| || || ||||| ||||||||||| || | | || |
atcacttcgtcagtgtatctcttgcttatgtttgtaaggaagtaccgttttacaagcagtggcggctactgttcttacactattgtcgcctcatttgcagCTACATGGGCAGTATCGGTGTACTTCGCATATGCGCGGACCTGGAAGCCTTTCAATCCCATTCTCGGTGAGACCTATGAGATGGTCGACAAGAATGGCCTMapped 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|88694164|gb|CI738202.1|CI738202EST: AGACAAAGCAGATGAATGCCAACACCCGTACATGCGTATGGCATATGCCT CTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTT
genomic: AGACAAAGCAGATGAATGCGAAGACCCGTACATGCGTATGGCATATGCCTgtaagttttg ... aacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTT
EST:
gi|29618292|gb|CB623304.1|CB623304EST: AGACAAAGCAGATGAATGCGAAGACCCGTACATGCGTATGGCATATGCCT CTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTT
genomic: AGACAAAGCAGATGAATGCGAAGACCCGTACATGCGTATGGCATATGCCTgtaagttttg ... aacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTT
EST:
gi|58601120|gb|CK011648.1|CK011648EST: AGACAAAGCAGATGAATGCGAAGACCCGTACATGCGTATGGCATATGCCT CTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTT
genomic: AGACAAAGCAGATGAATGCGAAGACCCGTACATGCGTATGGCATATGCCTgtaagttttg ... aacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTT
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:
68 (upstream exon),
74 (downstream exon)
Score:
55TTGATGGAATACTGTGAACTTTTAGACAAAGCAGATGAATGCGAAGACCCGTACATGCGTATGGCATATGCCTgtaagttttg ... aacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
cttttc CT-rich tract
ttttaacttaactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG