Sequence
atgc intronic sequence ATGC exonic sequenceACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g53880.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G057067_T02 (Zea mays), 5'ss of exon 4
ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaac--aacaaaaggacactgccacca-taatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag
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GAAAGATATTCTCTCAATTGTTGGATGGATCTGGCGAATATACCCTGGTCTACGAAGACAACGAAGGAGACAGGATGCTGGTAGGGGACGTGCCGTGGAAgtaagctt--------cctctgtcatttacggtccaaccgcaccctaccaacagaaaaacttctctaaaactgaatcgtcaaatactgctaacactaacttgaagaatgaaatatag----------------------------------------
upper sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G057067_T04 (Zea mays), 5'ss of exon 4
--------------------ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcattta--cagtttttactggca------tttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcacc------accaaaccatctaaattatttttcctgttctccaattcctgcag
|| ||||| | ||||||||||||||| ||||| |||||||| || || || ||||||| |||||||||||||||||||| ||||||||||| |||||||||| || || | | || | | | ||| || || || | | || | ||| || | || ||| | || | |||| || || ||||||| || || | | | | || |||||||
GGATATGTCTCCAACTGCTGGAAAGATATTCTCTCAATTGTTGGATGGATCTGGCGAATATACCCTGGTCTACGAAGACAACGAAGGAGACAGGATGCTGgtaggggacgtgccgtggaagtaagcttcctc-tgtcatttacggtccaaccgcaccctaccaacagaaaaacttctctaaaactgaatcgtcaaatactgctaacactaacttgaagaatgaaatatagtacaggcctactttgttgcaccatctgaa--gccttcctttgtatgtgatccctgcag
upper sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G057067_T01 (Zea mays), 5'ss of exon 4
ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcattta--cagtttttactggca------tttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcacc------accaaaccatctaaattatttttcctgttctccaattcctgcag
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GAAAGATATTCTCTCAATTGTTGGATGGATCTGGCGAATATACCCTGGTCTACGAAGACAACGAAGGAGACAGGATGCTGGTAGGGGACGTGCCGTGGAAgtaagcttcctc-tgtcatttacggtccaaccgcaccctaccaacagaaaaacttctctaaaactgaatcgtcaaatactgctaacactaacttgaagaatgaaatatagtacaggcctactttgttgcaccatctgaa--gccttcctttgtatgtgatccctgcag
upper sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G21460.1 (Glycine max), 5'ss of exon 3
ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag
| ||| | | || |||| ||| ||| ||||||||||| |||||||| || | |||||||||||||||||| ||||| || ||||| ||| |||||| | | || | || |||||| | || |||| | | || | || | || | | | | | | | |
AGAAATCCAATAAGGGTTTATTGGTTGGAAGTGGGGAATATACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGAGATGTGCCGTGGCAgtaagcatcttatcaatgtggatctgatgca-tttttatcttattctattcaatattatattcc-----atgactatagtttgatacaatattgccatgcagtgga------------------------------------------------
upper sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G02350.1 (Glycine max), 5'ss of exon 4
ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag
| ||| | || || |||||||| ||| || |||||||| |||||||| || | |||||||||||||||||| |||||||| ||||||||| |||||| | | | || | | | |||| |||| | | || ||| ||| | || | | || ||||| | | | ||| ||||
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTATACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatctta-------tcactatcaatcttatgtactattatttt--attttattcaatattatattatactatattgtacc-tcaccacttgatgtgtgagg-acca-------------------------------------------
upper sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G01800.1 (Glycine max), 5'ss of exon 3
ACAAAATATTTTATCAATT-GTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag
|||| || || |||| ||| ||| ||||||||||| |||||||| || | |||||||||||||||||| ||||| || ||||| ||| |||||| | || | || |||||| | || |||| | | || | || | | || || |||| | | ||
-AGAAATCCAATACGGGTTTATTGGTTGGAAGTGGGGAATATACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGAGATGTGCCGTGGCAgtaagcaccttatcattgtggatctgatgca-tttttatcttattctattcaatattatattcc--atgactatagtttgatac-attgccatgcagtggagta--------------------------------------------------
upper sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G43050.1 (Glycine max), 5'ss of exon 4
ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacact-gccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag
| ||| | || || |||||||| ||| || | |||||| |||||||| || | |||||||||||||||||| |||||||| ||||||||| |||||| | | | | | || | ||| | |||| |||| | || ||| | | | |||| | | | ||
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcagtatcaattttatgca-ctattattttattttattcaatactattatattatatattgtacctcaccacttgatgtgaggaccaat------------------------------------------------------
upper sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv04s0008g00220.t01 (Vitis vinifera), 5'ss of exon 4
-ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaag--tttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag
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CAAAAACCATGGCAG-GATTATTCGATGGAAGTGGTGAATATACTCTAGTTTATGAGGATAATGAAGGAGACAGAATGCTTGTTGGAGATGTCCCATGGCAgtaagcatctactaccaaacctacgcctccaaagtc----caaacattcaaaaatcaaacca-ttttcgacccaataaa-------tataagcatgata---gctgggcaatctc---tcatctgaattttaatatattccttgcag---------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|4714667|gb|AU055784.1|AU055784EST: TATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAA AGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCT
genomic: TATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgc ... attcctgcagAGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA