Sequence
atgc intronic sequence ATGC exonic sequenceAAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTGgtaaaactatattattttcttagcatatatgaacaccagtttgacagatgttgtgtttttctgcctccagtgagttaagcaatctactcaataagtagat...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g27350.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G458441_T01 (Zea mays), 5'ss of exon 6
---------------------------------------AAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTGgtaaaactatat--------tattttcttagcatatatgaacaccagtttgacagatgttgtgtttttctgcctccagtgagttaagcaatctactcaataagtagat
||||||| ||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| |||||| |||| ||||||||||||||| ||||||| || || ||||| |||||||| || || | ||| |
GTACATCCCATTACTAAAGGAGACATTTATGTTCCCACAAAGCTTGTGCATTTTAGGTGGAAAACCTGGTACATCAACATACATTGCTGGGgtacaggatgatagggctctctac-tagatccccatgaagttcagatggtaaacctgcatacattttatatttacttagcatgcatatgcatctatttcat-------------------------------------------------------
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G173682_T01 (Zea mays), 5'ss of exon 5
AAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTGgtaaaactatat--------tattttcttagcatatatgaacaccagtttgacaga-tgttgtgtttttctgcctccagtgagttaagcaatctactcaataagtagat
||||||||||||||| |||||||| ||||| || ||||| ||||||||||||||||| || || ||||| ||||||||||| |||||||| |||||| ||||||| || || ||||| ||||||| | || || ||| | | | || ||||| || || ||| | | ||||| | | | | ||| |
AAGCTTGGGCATTTTAGGTGGAAAACCTGGGACGTCAACATACATTGCTGGGGTACAAGAAGATAGGGCTCTCTACCTAGATCCCCATGACGTTCAGATGgtaaacctgcatacaatttgtatttaattagcatgcagatgcatcaatttcagaaaatgctgtgtattcctaccttt--taacttaag---tttgcaccatactt----
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 6
AAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTGgtaaaactatat--------tattttcttagcatatatgaacaccagtttgacagatgttgtgtttttctgcctccagtgagttaagcaatctactcaataagtagat
||||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||| ||||||| || || ||||| |||||||| || || | ||| | | | ||||| | || | | || | ||||| || |
AAGCTTGGGCATTTTAGGTGGAAAACCTGGTACATCAACATACATTGCTGGGGTACAGGATGATAGGGCTCTCTACCTAGATCCCCATGAAGTTCAGATGgtaaacctgcatactttttatatttacttagcatgcatatgcatctatttcataaacgttgtatagttttctaccttgtaacttaagttgagcaccatac--------
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G410085_T01 (Zea mays), 5'ss of exon 5
AAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTGgtaaaactatat--------tattttcttagcatatatgaacaccagtttgacagatgttgtgtttttctgcctccagtgagttaagcaatctactcaataagtagat
||||||||||||||| |||| ||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||| ||||||| | || ||||| |||||||| || || | ||| | | | | ||| | || | | || | ||||| || |
AAGCTTGGGCATTTTAGGTGTAAAACCTGGTACATCAACATACATTGCTGGGGTACAGGATGATAGGGCTCTCTACCTAGATCCCCATGAAGTTCAGATGgtaaacatgcatacattttatatttacttagcatgcatatgcatctatttcataaacgctgtatagttttctaccttgtaacttaagttgagcaccatac--------
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G442425_T01 (Zea mays), 5'ss of exon 5
AAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTGgtaaaactatat--------tattttcttagcatatatgaacaccagtttgacagatgttgtgtttttctgcctccagtgagttaagcaatctactcaataagtagat
||||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||| ||||||| || || ||||| |||||||| || || | ||| | | ||||||| | || | | || | ||||| || |
AAGCTTGGGCATTTTAGGTGGAAAACCTGGTACATCAACATACATTGCTGGGGTACAGGATGATAGGGCTCTCTACCTAGATCCCCATGAAGTTCAGATGgtaaacctgcatacattttatatttacttagcatgcatatgcatctatttcataaatgttgtatagttttctaccttgtaacttaagttgagcaccatac--------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|29646596|gb|CB651603.1|CB651603EST: CAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTG GCAGTTGATATTGCAGCTGATAACTTAGAGGCAGGCACTTCCTCATATCAC
genomic: CAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTGgtaaaactat ... tacatctcagGCAGTTGATATTGCAGCTGATAACTTAGAGGCAGGCACTTCCTCATATCAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGCTTGGGCATTTTGGGTGGAAAGCCTGGAACATCAACCTACATTGCTGGGGTACAGGATGACAGGGCGCTCTACCTAGACCCCCATGAAGTTCAGCTGgtaaaactatattattttcttagcatatatgaacaccagtttgacagatgttgtgtttttctgcctccagtgagttaagcaatctactcaataagtagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG