Sequence
atgc intronic sequence ATGC exonic sequenceGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttctatacttctatctggtccatatgacggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag...
Basic information
species | Oryza sativa |
transcript | LOC_Os12g30020.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G115670_T01 (Zea mays), 5'ss of exon 5
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagat---aatgttgtgttcta-tacttctatctggtccatatgacggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag--------
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GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGATAAGGTTTGGTGGCAGGATTTTGATGTCACACCACGGCAGCTTGAAGgttggtccttgtttgcaaagcctgtgatgaaacatttccttctgctttat-------tttgtatatatgttctg-----catacgacatgctttactgattgaattattatc
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G377311_T01 (Zea mays), 5'ss of exon 6
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagat---aatgttgtgttctatacttctatctggtcca-tatgacggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag--
||||||| ||||||||||||||||||||||||||| || |||||||||||||| ||| ||||||||||||| |||||||| || ||| |||| || |||||||||| | || | || | ||| || ||| | | || | | || | ||| ||| | | || | | |||| || | |
GCTATCTATTTGGCTGCTAAATTTCTCAAAGTGAATCTCCCATCTGATGGTGATAAGATTTGGTGGCAGGATTTTGATGTCACGCCACGACAACTTGAAGgttggtccttatttgcgaagttagtgagaaatgtttccactcgctctactttgtctatttgt-----tctgcatatgttgtgattgt-tattgattgaattggcac
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G17960.1 (Glycine max), 5'ss of exon 5
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttctatacttctatctggtccatatgacggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag---
|| || || | ||||| || ||||| || |||||||| ||||| ||||| |||||||| |||||||| ||||||||||| |||||| | || |||| |||||||| || | | || || ||| | | || | | ||| | | | | | | || || | | | |
GCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCAGATGGGGAGAAGGTCTGGTGGCAAGAGTTTGATGTCACTCCACGCCAATTGGAGGgttggtgtct---ttttattcagtactagtcgtataaagaaatgaggaaaaaaagtaccatctcattgtcatctctcttttctatcattcctcttatgcttat
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G02860.1 (Glycine max), 5'ss of exon 6
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttc-tatacttctat--ctggtccatatga-cggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag
|| || || | ||||| || || | ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| || ||| | || | || ||| |||| | | || || || | || | | || | | || | || |||| | | || | ||| |
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatttgtttgggtagccttttgtgttcccttg-gtttaatgcattatgatcatttctgc---
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G35010.1 (Glycine max), 5'ss of exon 5
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttc-tatacttctat--ctggtccatatgacggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag
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GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAATTTGATGTCACCCCACGTCAATTAGAGGgtcggtgtcatctcctcaattcatttgcatgctaataaaattgatctgtttggatggccttgt--gttcccttggtttaatgcattatgataatttctgcca-
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G41040.1 (Glycine max), 5'ss of exon 5
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataat--gttgtgttc-tatacttctatctggtccatatgacggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag
|| || || | ||||| || ||||| || |||||||| ||||| ||||| |||||||| |||||||| ||||||||||| |||||| | || |||| |||||||| || || | || | || |||| || || | | | | ||| || |||| | | | | || || | |
GCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGATGGGGAGAAGGTCTGGTGGCAAGAGTTTGATGTCACTCCACGCCAATTGGAGGgttggtgtctttttattcagtactagtcgtataaagaaatgaggaaaaaaaagtaccatctcattatcatctctcttttttatc-tttcctcttattcatg--
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G02880.1 (Glycine max), 5'ss of exon 5
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttc-tatacttctat--ctggtccatatga-cggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag
|| || || | ||||| || || | ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| || ||| | || | || ||| |||| | | || || || | || || | || | | || | || |||| | | || | ||| |
GCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGATGGTGAGAAGGTTTGGTGGCAAGAGTTTGATGTCACCCCACGCCAATTAGAGGgtcggtgtcatcccctcaattcatttgcatgctaacaaaattgatctgtttgggtagccttttgtgttcccttg-gtttaatgcattatgatcatttctgc---
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G45190.2 (Arabidopsis thaliana), 5'ss of exon 8
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttctatacttctatctggtccatatgacggtttacaacaatctcctga-gttttaaaccgcatattttttttaacgag-----
|| || ||| | || || || || || ||||||||| | ||||| ||||| ||||||||||||||||| || |||||||| || || ||||| ||||| ||| || | ||| | | | | |||| | | |||| | | || | | | ||| || | | | |||| |
GCAATATTTCTTGCGGCCAAGTTCCTTAAAGTGAAGTTACCATCAGATGGAGAGAAGGTTTGGTGGCAAGAATTTGATGTCACACCCAGACAACTGGAGGgtatgtac---aatatgaattgacttgacaattcttgtttccttgtttgacttccattccctttttctttatgatttcaagagtaatcgtcttttgtatatctcag
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 5'ss of exon 5
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttctatacttctatctggtccatatgacggtttacaacaatctcctgagttttaa-accgcatatttttt--ttaacgag
|| || || | ||||| || ||||||||||||||||||||||| ||||||||| ||| |||||||| || |||||||| || ||| | ||| |||| ||||||| | | || || | | | ||| || || ||| || | ||| | ||| | | | |||||| | | ||
GCCATTTTCCTTGCTGCCAAGTTTCTCAAAGTGAAGCTTCCATCGGATGGTGAGGTGGTCTGGTGGCAAGAATTTGATGTCACCCCACGCCAGTTGGAGGgttggtttcctccccttttttggtgtaaaattggtatggactcaatgggacagtcttcaaacagctctgtggcactgttgctgcatatggatggactgac---
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 5'ss of exon 5
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtg-cctagataatgttgtgttctatacttctatctggtccat-atgacggtttacaacaatctcctgagttttaaaccgca--tattttttttaacgag
|| || || | ||||| || || |||||||| ||||| ||||| |||||||||||||| |||||||||||||| ||||| || ||| | || | || ||||||| ||| | || || ||| | || || | | || ||||| | | | | ||||| | | || || ||| | |
GCAATTTTCCTTGCTGCCAAGTTCCTCAAAGTAAAGCTCCCATCAGATGGTGAGAAGGTCTGGTGGCAGGAGTTCGATGTCACCCCACGCCAATTAGAGGgttggtttcctctcttattttctgtagcagcattata---gacctatgatgacagagtgccttcccttttctctttttatatgataaacatattcattatcaa-
upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S264_33V6.3 (Physcomitrella patens), 5'ss of exon 6
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggt-gcctagataatgttgtgttctatacttctatctggtccatatgacggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag
|||||||| |||||||| || ||| | |||||||| || || ||||| || ||||| ||||||||| ||||||| || || || |||||| |||||||||||| ||| | | | || || | | | ||| | | ||| | | | || || | | ||| |
GCTATCTTCTTGGCTGCCAAGTTTTTGAAAGTGAATCTGCCCAAAGATGGAGACAAGGTGTGGTGGCAGCAGTTTGAAGTAACCCCTAGACAGTTGGAAGgttggtcacctcgttcacattccagcagatgcctaaactctactatcatgctactatccaagctctatttta--ctaaagccttgtctggtttgcag----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
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGATGGTGAGAAGGTTTGGTGGCAGGAGTTTGATGTGACTCCAAGACAGCTGGAAGgttggtgcctagataatgttgtgttctatacttctatctggtccatatgacggtttacaacaatctcctgagttttaaaccgcatattttttttaacgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG