Sequence
atgc intronic sequence ATGC exonic sequenceGGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44900.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 1
lower sequence: AC197122.3_FGT003 (Zea mays), 5'ss of exon 1
GGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag
|||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||||||||| ||||||| |||||| | ||||||| || |||| |||| || | | | || || || | | | | || |
-------ATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTGAAGAAGgtccaggagggcgtcgatgtctttgacagcatctggaataaggcacgccccca---gcgccctccctccgtttacccggcccctgccagaactttttctcgcgatttttgttgattttttttg----tttgggggcag-----------------------------------------------------------------------------
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G26850.1 (Glycine max), 5'ss of exon 1
GGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag
|| | ||||| || || || || || || |||||||| || ||||| || |||||||| ||||| |||||||| |||||||| |||||||||||||||| | || | | | | || | || | ||| | | | || |
GGTGGAAATGGGAGCGAGTCGAAAACTCCAAGGCGAGATTGATCGCGTTCTTAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcctcttctcttcttcgattatttcgaatt--ttctcctgtttttggctcacacatggcgttggtgcgttag------------------------------------------------------------------------------------------------
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G04690.1 (Glycine max), 5'ss of exon 1
GGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag
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-------ATGGGTGCGAGTAGAAAACTCCAGGGAGAGATAGATCGCGTTCTCAAGAAGGTTCAGGAAGGCGTTGAAGTCTTCGATAGCATCTGGAACAAGgtacttcatttgtttctctcactttttttttatttaaaagttttcagtttttgttcattgtttttagattttcattg-cttcggaacaaaatgacgggtttggtttggggatag-----------------------------------------------------------
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 1
GGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctcc--ctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag
||| | ||||| || || || ||||| ||||||||||| || || || ||||||||||| ||||| |||||||| |||||||| |||||||||||||||| | | | | | | | || ||| | | | | ||| | | | || |
GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtc---attcttctcttctttg-attatttcgattttcttctgttttcgactcacacatggcgttgctgcgttag------------------------------------------------------------------------------------------------
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G04690.2 (Glycine max), 5'ss of exon 1
GGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag
| | | ||||| || || | || || ||||| ||||| || ||||| ||||||||||| ||||| ||||| || |||||||| |||||||||||||||| ||| | |||| | | | | | | | || | | | | | || | | ||| | || || || | |
GTAATCGATGGGTGCGAGTAGAAAACTCCAGGGAGAGATAGATCGCGTTCTCAAGAAGGTTCAGGAAGGCGTTGAAGTCTTCGATAGCATCTGGAACAAGgtacttcatttgtttctctcactttttttttatttaaaagttttcagtttttgttcattgtttttagattttcattg-cttcggaacaaaatgacgggtttggtttggggatag-----------------------------------------------------------
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ20408 (Selaginella moellendorffii), 5'ss of exon 1
GGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag
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-------ATGGGCGCGACGCGGAAGCTCCAGGGCGAGATCGATAGAGTTCTCAAGAAGGTCCAGGAGGGCGTGGATGTCTTCGACAGCATCTGGAATAAGgtatggaaatctatggcgtcgcctcgccattgatcgatcgagaatttttttttcttctcgcag--------------------------------------------------------------------------------------------------------------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|58665828|gb|CK054514.1|CK054514EST: TCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAG GTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTC
genomic: TCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactccccc ... gcttgtacagGTCTACGACACCGAGAATGCGAACCAGAAGGAGAAGTTCGAGGCCGACCTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctccctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG