Sequence
atgc intronic sequence ATGC exonic sequenceGTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g04340.2 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G155836_T01 (Zea mays), 5'ss of exon 10
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagctttccttttttt-ttaccaccag----------
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GTTCTGGGCACACCCACACGTGAAGAAATTAAGTGCATGAATCCAAATTATACCGAGTTTAAATTCCCGCAAATCAAAGCTCACCCATGGCATAAGgtaggg-------attttgtattggattgtgtgccctctcttcctgtccctaacctccaccaaggttgacatcttccattgatgtctttctgtgctag
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA02G01220.2 (Glycine max), 5'ss of exon 10
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag
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GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAGgtattgtaatgttatatt-tgcctgtccatttatgtgatatttcattgtgatattcatatata-tgaaccttcattatcag------
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 10
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagcttt-cctttttttttaccaccag
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GTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAGgtattataatgttatttt-tgcatgtctatttacatgttatttcattatgatattcatatatatatgaaccttcatcttcag------
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 10
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacct----aatgtagctttccttttttttt--accaccag----
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GTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAGgtactggatagaagcaggatattacttcaattctgctatgcttc----ttacaacctcacgaatattgattttcattcttattgtacctcctatcag
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgta------------gaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag----
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GTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAAgtatgtggtctttgtgaatgcactgtttccatcttgggct-ttggtagtgtagtccagaagtggagat--gtacgaccgtgttttcgtgtgagcggtgggttt
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgta------------gaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag--
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GTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtctgtgtgaatgcactgttttcatcttgggct-ttggtagtgtagtccagaagtggagatgtacgaccgtgttttcgtgtgtgagcggtgggt
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtt----tattttttattt-tagggttgaaacctaatgtagc---tttcctttttttttaccaccag-----
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GTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAGgtacggctggtctgtgtgttagtggtctggtatggtgctttggagatgtactgtaacagttgattggaaagcgttacctgtattcataataacggtgatt
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttgg--actgtttattttttattttagggtt-gaaacctaatgtagctttcctttttttttaccaccag-----------------------------------------------------------------------------------------------------
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GTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAGgtatg-gtttgtatgtttgggttagctatttttagtggtctattatataatttgataggaattatccgtgtcctcgatattggtgattttgaatttggttggttggacgctgctactcgttgtgattgggagaatggagcgtgttgcattgaccttagcaacgtgcgaattgattggttctgtggtggcag
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaa-------gaaaataatcttatgttggactgtttatttt--ttattttagggttg-aaacctaatgtagctttcctttttttttaccaccag-----------------------------------------------------------------------------------
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GTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcag
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 10
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatct-tatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag
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GTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGgtaagagcaatcatccggtatatctctctctctgtctctcttgatgtggctcgttgacag----------------------------
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 10
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatct-tatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag
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GTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGgtaagagcaatcatccggtatatctctctctctgtctctcttgatgtggctcgttgacag----------------------------
upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ04915 (Selaginella moellendorffii), 5'ss of exon 9
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag
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GTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAGgtgcgtaggcaacttctt-tgttggggcggtcgtttac-gtagtaacgtggcag---------------------------------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|58671594|gb|CK060280.1|CK060280EST: ATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAG ATCTTCTATAA
genomic: ATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaa ... ttaccaccagATCTTCCATAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTCTGGGTACCCCTACACGAGAGGAGATTAAGTGCATGAACCCAAATTACACCGAGTTTAAATTTCCGCAAATCAAAGCTCACCCATGGCACAAGgtagaagaaaataatcttatgttggactgtttattttttattttagggttgaaacctaatgtagctttcctttttttttaccaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA