Sequence
atgc intronic sequence ATGC exonic sequenceGACTATGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAGgtagcccgcgtcctgtctctccgtggttccggcatttcgtcgaacacctagcggtgggaatgcaggttttctgcgccaggaaatttgatttttttttttcttttctgtgtgttgcttcttgacgtttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g38580.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G112865_T02 (Zea mays), 5'ss of exon 2
GACTATGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAGgtagcccgcgtcctgtctctccgtggttccggcattt--cgtcgaacac----ctagcggtgggaatgcaggttttctgcgccaggaaatt--tgatttttttttttcttttctgtgtgttgcttcttgacgtttcag
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GACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtatttt---ttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttc-----gtttcag
upper sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G175875_T01 (Zea mays), 5'ss of exon 1
-----GACTATGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAGgtagcccgcgtcctgtctctccgtggttccggcatttcgtcgaacacctagcggtgggaatgcaggttttctgcgccaggaaatttgattttttttt--ttcttttctgtgtgttgcttcttgacgtttcag
||| ||||||||||||||||||||||| ||||| |||||||| ||||| || |||||| | | || | | | ||| |||| || | | |||||| || || ||| || |||||| ||||| | | || || |||| ||| | |
GGTAGGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACTACCGTTGCCAAGGTA-------CTTTCTTTCGCGGCGTTTC------TTCGAGCAAGGGCGTGTGgtgggcgggc-ggatttgtgttccaggagtggtgattgtgaatgagtttcctttgctgtggtgcgtttcag--------
upper sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 1
---------------------------------------------GACTATGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAGgtagcccgcgtcctgtctctccgtggttccggcattt--cgtcgaacac----ctagcggtgggaatgcaggttttctgcgccaggaaatt--tgatttttttttttcttttctgtgtgttgcttcttgacgtttcag
||| ||||||||||||||||||||||| ||||| |||||||||||||| || |||||| | || |||||| | |||| ||| | |||| || || | |||||| ||||| ||| || |||||| | ||| || | ||| || || |||||| |||||||
TGCGTCGCCTTGCCGTTGATCTCACTGGATTTGTCTCCCCGGCAGGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAGgtatttt---ttctctctctctcgtataccggtgttttccatcgaccagggggcttgtggtgggcgggcaggatttgggctccaggaggggggtaattgttaactgcgtttcctttgccgtgcttc-----gtttcag
upper sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 5'ss of exon 2
GACTATGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAGgtagc-ccgcgtcctgtctctccgtggttccggcatttcgtcgaacacctagcggtgggaatgcaggttttctgcgccaggaaatttgatttttttttttcttttctgtgtgttgcttcttgacgtttcag
|| |||||||||||| |||||||||| ||||| || || |||||||| || |||||| | || |||| | || || || | || | | | || ||| |||| | | | ||||| || | ||
AACAATGGTGTCGCAGTTGGTGAAGCACGAGCGCATTGAAACCACCGTTGCCAAGgtaaaactgcttcctctttcaatgttttttgtttacatctttgtttgttt-gccgtgaaaatgtcgagcgatggaa--gacgagcttgatgttgaatgcattt----------------------------
upper sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S194_11V6.1 (Physcomitrella patens), 5'ss of exon 2
GACTATGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAGgtagcccgcgtcctgtctctccgtggttccggcatttcgtcgaacacctagcggtgggaatgcaggttttctgcgccaggaaatttgatttttttttttcttttctgtgtgttgcttcttgacgtttcag
|| | | ||||||||||| ||| |||||||||| ||||||||||| || | ||||| ||| | | | ||| || | || | | | | | | || ||||| || | | | |||| |||| ||| || | |
GAATCTCGTGTCGCAGCTTGTGCAGCATGAGCGAATCGAGACCACTGTTCCTAAGgttaggggcggtgcaacgcctctctgttgcg-----ttgttgcggatttggggttttc--tgtgggttt--tgttcaaatcattttgggcttttgagttcgga---gtatat------------------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|27547785|gb|CA766051.2|CA766051EST: TGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAG GCGAAGGAGGTGCGGACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAG
genomic: TGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAGgtagcccgcg ... gacgtttcagGCGAAGGAGGTGCGGACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACTATGGTGTCGCAGCTGGTGAAGCATGAGCGGATCGAGACCACCGTCGCGAAGgtagcccgcgtcctgtctctccgtggttccggcatttcgtcgaacacctagcggtgggaatgcaggttttctgcgccaggaaatttgatttttttttttcttttctgtgtgttgcttcttgacgtttcag
- - - - - - GCAGCT
- - - - - - CAGCTG
- - - - - - - - - - TGAAGC