Sequence
atgc intronic sequence ATGC exonic sequence...tatacttatttaactttttgataatacaatttgatcatgacacattcctttctgggttcttgttaaatcagataataatgcatgtctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os12g30020.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 5
tatacttatt--taactttttgataatacaatttgatcatgacacattcctttctgggttcttgttaaatcagataataatgcatgtctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC
|| ||||| | | |||| || ||||| || || ||||| | | | ||| | ||| | || || ||| | || | |||||||||||||||| ||||||| |||||||||||| || ||| || || |||||||||||| || || |||| |||||||| |||||||||||| |||| |
cctaattattagttatttttaattataacaatgtggtc-tgacatttgctagttcaagttgc-atctaataatgaaaacatatatgccctccataattgcagAAGTTAGCAGTCAAATGATGGAGCTGTATGTTCAGAACCGTACACCACAGGCACAACAATCACAGGGAAGCGAAGCTGAGGGGAGCTCTGCTGGTGTGCG
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 6
tatacttatttaactttttgataatacaatttgatcatgacacattcctttctgggttcttgttaaatcagataataatgcatgtct----cccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC
|| |||| | | | || | || || | | | || ||||| ||| || ||| ||| |||| |||| | || |||||||| ||||||| |||| || ||||| |||||||||||||| || || | ||||||||| | || || |||| |||||| || |||||||||||| ||||
---acctattataataatggagtctggcatgtgctttttatctcttggtttctaagttgc-atttgatctgatgataaagcatattcgttgtccaccattgcagAGGTTAGCAGTCAATTGCTGGAGTTGTATGAGCAAAACCGTACAACGCAGGCACAATCATCACAGGGAAGTGAAGCGGAGGGGAGCTCTGCTGGTGTGTG
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G17960.1 (Glycine max), 3'ss of exon 5
-tatacttatttaac--tttttgat---aatacaatttgatcatgacacattcctttctgggttcttgttaaatcagataataatgcatgtctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCC-ATGGAAATGAAGCT---GAAGGGAGCTCTGCTAGTGTTCC
|| || || || | | || ||| | | |||| ||| | | | |||||| || | | || || | | | ||||||||||||| ||||||||||| ||||||||||| ||||| | ||| | |||| | | | ||| || || | || | |||| | |
ttagacaggttcaatggtactaaatttggatatcgtattatcacaacataagacctatgttgttcttatttatttgtttattatta------ttattattttgcagAAGTTAGTAATCAAATGTTAGAGCTGTATGAACAAAATCGAATGCCACCTTC-CAACGATGTCGAAGGAGGTGGGACTTCCAATCAGACCACTGCAAAAGC---
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 5
tatacttatttaactttttgataatacaatttgatcatgacacattcctttctgg-gttcttgttaaatcaga-taataatgcatgtctcccttgatt-----gcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCC-ATGGAAATGAAGCT---GAAGGGAGCTCTGCTAGTGTTCC
|| |||| ||| | | | || ||| | | ||| | | |||| | | | ||| |||| || | | || || ||||||||||| ||||||||||| ||||| ||||| ||||| | ||| | ||| | | | ||| || || | ||| | |||| | |
--tatttatctaaat-----agagactggttcaatcgtactaaatttggatatcatattctcataacacaagactaatgttgttcttattttttattttttttgcagAAGTTAGTAATCAAATGTTAGAGCTCTATGAACAAAATCGAATGCCACCTTC-CAATGATGTCGAAGGAGGTGGGACTTCCAATCGGACCACTGCAAAAGC---
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 5
tatacttatttaactttttgataata-caatttgatcatgacacattcctttctgggttcttgttaaatcagataat------aatgcatgt---ctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC
| || ||| || | | ||| | ||| | | ||| || || | | ||| | | | ||| | |||||||||||||||||||||||||||| || || ||||| || | ||| ||||| | | | | | | || || | | || | |
----------cagtttattgctatgagtagtttaacaatgggttgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAAGTTAGCAATCAAATGTTGGAACTCTACGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 6
tatacttatttaactttttgataata-caatttgatcatgacacattcctttctgggttcttgttaaatcagataat------aatgcatgt---ctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC
| || ||| || | | ||| | ||| | | ||| || || | | ||| | | | ||| | ||||||| |||||||||||||||||||| || |||||||| || | ||| ||||| | | | | | | || || | | || | |
----------cagtttattgctatgagtagtttaacaatgggctgtccttttgtgtgtctgtatgcttctgtatatccttctcagttcttgtgggtattttctcttgcagAGGTTAGCAATCAAATGTTGGAACTCTATGAGCAGAATAGACTTCCACCAGCACAGGGAAGTGAAGTAGAAGGAAGTGCTGGAGGAACAAGAGCTGCTTC
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 5
--tatacttatttaactttttgataatacaatttgatcatgacacattcctttctgggttcttgttaaatcagataataatgcatgtctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC---------
|| ||| ||| | || | | | ||| | | ||| || || | || ||| | | ||||||| ||||||||||||||||||| ||||||||||||||| | | | || | || || | |||| |||| | | | | ||| |
gccatgggcatt-gctgtttcattcatggggctgtccttttgcgtcttcttcgggtgaacctttttggatttccctaacat-tatggttatttgtcttgcagAGATTAGCAATCAAATGTTGGAACTGTATGAGCAAAACAG---------AGTGCCTCCACCTCAAGGGAGTGAAATGGAAGTTAACGCCAGTGGTGGACTAAACCATAG
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S119_132V6.1 (Physcomitrella patens), 3'ss of exon 5
tatacttatttaactttttgataataca-atttgatcatgacacattcctttctgggttcttgttaaatcag--ataataatgc-------atgtctcccttgatt-gcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCG--TCCCATGGAAATGA----AGCTGAAGGGAGCTCTGCTAGTGTTCC
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---gtgaatctcacgttctcatacttttcgtttaatcagaaagctgcattatctgcattatagtatatgcaatcatcaaaatacttcactgataattcgtttgttttgcagAAGTAAGCAATCAAATGTTGGAGCTGTACGAGCAGAACAAAAC--CAATGGTCCAACGGGTTCGCTTGCCAATGATCCAAGTCCCAGCGAATTGAACCGGGG----Mapped 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|29678245|gb|CB674520.1|CB674520EST: GTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAG AAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGG
genomic: GTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcct ... ttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctttctgggttcttgttaaatcagataataatgcatgtctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC
ccttgat putative branch site (score: 5)
tgtctccctt CT-rich tract
ttaaatcagataataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatacttatttaactttttgataatacaatttgatcatgacacattcctttctgggttcttgttaaatcagataataatgcatgtctcccttgattgcagAAGTTAGCAATCAAATGTTGGAGCTGTATGAGCAAAACTGTGCAGCACAGGCACAACCGTCCCATGGAAATGAAGCTGAAGGGAGCTCTGCTAGTGTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT