Sequence
atgc intronic sequence ATGC exonic sequence...attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11140.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtcc-ttatagattgtaactgattttgagc-----agGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
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----gtcaagctgcg-attgcaagcttttagctggaggctgtgacagtttat-ggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 13
------------------------------------------------------attagttggtgtgtacatggaaagtttgtgtgcacagg-atacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
||| | | | || || ||| | | | ||| | ||| || | ||| | ||| ||| | | | | | ||| | |||| | ||| || || || || |||||||| ||||| || || |||||||| || |||||||| ||||| || |||| || || || |||||||||||||||||
gttaatcccctgaagtatttattcttcatgtattgtgtctttgggatggcgataattggcttgagtttagatgatcacatgttttgcttttgcatattttgactggttatgtttaaactgtcttcttact-tgtatttggattgatccttt-tagGTACCCAGTACTTGCAGCAATCCTATAAAGTCAGTGATTCATTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
|| |||| | ||||| | | | || | || | | | | | | | | | | || | || | |||| || || ||| || ||||| || ||||| || ||||||||||| ||||||||||| ||||| ||||||| |||||| || || || ||| | |||||
--------gttagtacctctaaagtatatattggcaatgtcaatttggcaaatttcaat---tttgttttccgctgactatgatcttggactc----cagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
|| | | || | | | | | | || | ||| || || | | | || || | | || | ||||||| || ||| ||||||||||||||||| || || || |||||||||||||||||||| || ||||||| ||| || || ||||| || | |||||
----------gtattcttgttttactccttttgaatg--caggtgtaacagttatttccgttttatctctgtttcacag-ttttcatcatttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 13
attagt-tggtgtgtacatggaaagtt-tgtgtgcacaggatacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
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gtcagtgtgacttatttaaaaccaatcattttttgagacaatgacttcttttatgattgtta--tctgtctcttttaacctctgttaatttactgaatatagGCACGCAATATTTACAGCAGTCCTATAAAGTCAGTGAGTCATTTCCATTTAAGTGGATAAATAAAAAATGGAGAGAGGGTTTCTATGTTACTGCTATGGC
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 13
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
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----------gttagtctaacatatttggct------gatggatttctatgacaaaatttatcta---tattttgcttgacttcatttcattgactccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCAAGTGGATAAATAAAAAATGGAGGGAGGGTTTCTATGTCACCTCTATGGC
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagca-tgtccttatagattgtaactgattttga-gcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
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------------------------------------------gtattgtcgctgttattg-atggccactggcattgtcgctgacgcgtgtttcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagca-tgtccttatagattgtaactgattttga-gcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
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------------------------------------------gtattgtcgctgttattg-atggccactggcattgttgctgacgcgtgattcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCMapped 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|29626917|gb|CB631928.1|CB631928EST: TTCATTAGCAGGTGCAAACAATGGCAGTTCTCTGGTGGTCATGTCAAGAG GGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCA
genomic: TTCATTAGCAGGTGCAAACAATGGCAGTTCTCTGGTGGTCATGTCAAGAGgtatatcatt ... ttttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCA
EST:
gi|218483459|gb|FG953851.1|FG953851EST: TTCATTAGCAGGTGCAAACAATGGCAGTTCTCTGGTGGTCATGTCAAGAG GGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCA
genomic: TTCATTAGCAGGTGCAAACAATGGCAGTTCTCTGGTGGTCATGTCAAGAGgtatatcatt ... ttttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
ttgttatta TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtccttatagattgtaactgattttgagcagGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG