Sequence
atgc intronic sequence ATGC exonic sequence...aatatgtgtctaaattcctgttgcattcatgcttgaccagaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01850.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 3
aatatgtgtctaaattcctgttgcat-tcatg-cttgacca-gaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
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---ccctttcctcatttccattatatctcataacctgaaaatgaatgaggtgcaggtgcttgtgggtgcattctgaaatgtaactattttcttctttctccagTCATACCTCTACCAGATACTCCACGGTGTTGCGTACTGCCATTCTCATAGAGTTCTTCATCGAGACTTGAAACCTCAAAACTTATTGATAGATCGGCGCA
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 3
---aatatgtgtctaaattcctgttgcattcatgcttgaccagaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
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ttatttgcctttcctcatttccattgtatctat---taaccagaaaatgaatgaggtgcctgtggatgcattttgaaatgtgactgttttctttgttctccagTCATACCTCTACCAGATACTCCGTGGCGTTGCGTACTGCCATTCTCATAGAGTTCTTCACCGAGATTTGAAACCTCAGAACTTGTTGATAGATCGGCGTA
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 3
aatatgt-gtctaaattcctgttgcattcatgcttgaccaga-aagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
||| | ||| | | || ||||| | | || |||| || | || | || |||| | | | ||||| ||| | || ||||| || ||| | ||| |||||||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||||||||| ||||
tttattttgtcatgggttatattagggagatgctaattttggtgaaaataccagttagtttggatttaaattttgaattc--tttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 2
aatatgtgtctaaattcctgttgcattcatgcttgaccagaaagtgtattagtttattgtggttgcatcttggaatgtgactgtt----ttctt--------ctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
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--------tccaccttatcat-gcatcgttaattga--atatgttttattt-tttattgtggtttcaaaacaagatgagctaattaaaatttttaaatgatgctttctgcagATGTTCCTGTACCAAATTCTCTGTGGCATTGCATACTGTCATTCACATAGAGTTCTTCATCGAGACTTAAAACCACAGAATTTGTTGATAGATCGCAGCA
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 3
aatatgtgtctaaattcctgttgcattcatgcttgaccagaaagtgtattagtttattgtggttgcatcttggaatgtgactgttt---tctt---------ctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
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--------ttccaccttattatggatcgttaattga--atacattttatt--tttatcgtggtttcaaaacaagatgagctaatttaaatttttaaatgatgctttctgcagATGTTCCTGTACCAAATTCTCTGTGGCATCGCTTACTGTCATTCACGTAGAGTTCTTCATCGAGACTTAAAACCACAGAATTTGTTGATAGATCGCAGCA
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 3
aatatgt-gtctaaattcctgttgcattcatgcttgaccaga-aagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
||| | ||| | | | | ||||| | | || |||| || | || | || |||| || | | ||||| ||| | || ||||| || ||| | ||| |||||||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||||||||| ||||
tctattttgtcaagggttatataagggagatgctaattttggtgaaaataccagttagtttggatttaaaatttgaattc--cttaatgatcctttctgcagATGTTCCTTTATCAAATTCTCTGTGGCATTGCTTACTGTCATTCACATAGAGTTCTTCATCGAGACTTGAAACCACAGAATTTGTTGATAGATCGCCGTA
upper sequence: LOC_Os03g01850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 4
-aatatgtgtctaaattcctg-ttgcattcatgcttgac-cagaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
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tttttgatgtctatattttaaattattttcatatttatttctgggcatatgcttggagataatggt-gcgatggggcttctgacacttgagtccttt--gcagATGTTCCTGCATCAGATTCTCCGTGGTATTGCTTATTGTCATTCTCATAGGGTTCTTCATCGAGATTTGAAGCCCCAGAACTTACTCATAGATCGTCGTAMapped 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|29662032|gb|CB658307.1|CB658307EST: TCCAGAGTTTGCAAAAAACCCCACTTTAATTAAG TCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGA
genomic: TCCAGAGTTTGCAAAAAACCCCACTTTAATTAAGgtgagcggcc ... ctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
ctgttttcttctttcg CT-rich tract
agtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatatgtgtctaaattcctgttgcattcatgcttgaccagaaagtgtattagtttattgtggttgcatcttggaatgtgactgttttcttctttcgccagTCATATCTCTATCAGATACTCCGCGGCGTTGCTTACTGTCATTCTCATAGAGTTCTTCATCGAGATTTGAAACCTCAGAATTTATTGATAGATCGGCGTA
- - - - - - - - -ctgttgc
- - - - - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - -accagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgtg