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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTGAGAAGGAGTTCAAGGTGGAGGTTGAAGCGATCGGGCGTGTTCGGCATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaaatctcttcatcaattttgtgcattattattccctctctgattaatggatgttttactcacattgccgttttggttgaacag

Basic information

species Oryza sativa
transcript LOC_Os03g03410.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G014366_T03 (Zea mays), 5'ss of exon 2
AGGCTGAGAAGGAGTTCAAGGTGGAGGTTGAAGCGATCGGGCGTGTTCGGCATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaaat--------ctcttcatcaattttgtgcattattattccctctctgatt-----------aatggatgttttactca---cattgccgttt-tggttgaacag
|||| ||||||||||||||||||||||| ||||| || || ||||||||||| || |||||||| || ||||| || ||||| ||||| || ||||| |||||  |||  ||        |||||| ||| ||  || |  |   |    ||||| | ||           |||||| |  | | ||    || || ||| | || ||||||||
AGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCTTACAGgtatgatggcatattgctatctcttcttca-ttcggtccggtgacacctactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacag

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G317938_T01 (Zea mays), 5'ss of exon 2
AGGCTGAGAAGGAGTTCAAGGTGGAGGTTGAAGCGATCGGGCGTGTTCGGCATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgta----------------caatgaaatctcttcatcaattttgtgcattatta-----ttccctc----------tctgattaatggatgttttactc---acattgccgttttggt-------tgaacag
|||| ||||||||||||||||||||||| ||||| ||||| ||||||||||| || |||||||| || |||||||||||||| |||||||| ||||| |||||                || || ||||||||| ||  ||  ||| |    ||     ||| |||          ||| | | ||||| | ||   ||   | ||  |   | ||||       |||||||
AGGCCGAGAAGGAGTTCAAGGTGGAGGTGGAAGCAATCGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTCGGCTACTGCGTAGAGGGTGCTTACAGgtatgtgtgttggcaggcacattgcaatctcttcttcg-ttcggtggacacctagttgcttctctcaatttagggttctcaatgatggaagcttgcttctgtatatcactactatggtctatgcttgaacag

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G01330.1 (Arabidopsis thaliana), 5'ss of exon 2
AGGCTGAGAAGGAGTTCAAGGTGGAGGTTGAAGCGATCGGGCGTGTTCGGCATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaa-atctcttcatcaattttgtgcattattattccctctctgattaatggatgttttactcacattgccgttttggttgaacag-
| |||||||||||||| |  ||||| || ||||| |||||||||||  |||||||||||||||||||  |  | || ||||| || || || || || |||||  |  || |   |  |||   |  |  | | | ||  ||  |   || ||      |   | | ||  |  |   ||    ||   |   
AAGCTGAGAAGGAGTTTAGAGTGGAAGTGGAAGCTATCGGGCGTGTAAGGCATAAGAATCTCGTTAGGCTATTAGGATACTGCGTCGAAGGAGCATACAGgtaagaaaaagaaacccgcatgcttgatacggact-ttgctcggtacttgttttgaactttgataagtcttaacgtttttggaattcctctag

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 5'ss of exon 2
AGGCTGAGAAGGAGTTCAAGGTGGAGGTTGAAGCGATCGGGCGTGTTCGGCATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaaatctcttc-atcaattttgtgcattattattccctc----tctgattaatggatgtttta----ctcacattgccgttttggttgaacag
| ||||||||||| ||||| |||||||||||||| || || || || ||||| |||||||| ||||| ||||| || |||||||  ||||| ||||| |||||     |    |||||    || |     || |    || | |     ||  |  ||   |  ||||     ||  ||||    ||||  |||   ||
AAGCTGAGAAGGAATTCAAAGTGGAGGTTGAAGCCATAGGCCGGGTCCGGCACAAGAATCTTGTTAGGTTGCTGGGATACTGTGCTGAGGGAGCTTACAGgtattgctacccatcttctgctaaatcctgacactgggttttcttgaggatccaaaaaactaacattttttcatctttcatttgttttttttttgtctag

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|58687074|gb|CK075761.1|CK075761
EST:     CATAAGAATCTCGTTAGA-TGCTCGGCTACTGTGTAGAGGGCGCTTATAG                         GATGCTCGTGTATGAGTATGTAGACAACGGCAATCTTGATCAATGGCTTCA
genomic: CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaa ... ggttgaacagGATGCTCGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTCA
EST: gi|58693474|gb|CK082161.1|CK082161
EST:     CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAG                         GATGCTCGTGTATGAGTATGTAGACAACGGCAATCTTGATCAATGGCTTCA
genomic: CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaa ... ggttgaacagGATGCTCGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTCA
EST: gi|58680836|gb|CK069523.1|CK069523
EST:     CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAG                         GATGCTACGTGTATGAGTATGTAGACAACGGCAATCTTGATCAATGGCTTC
genomic: CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaa ... ggttgaacagGATGCT-CGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTC
EST: gi|300215530|gb|HO088156.1|HO088156
EST:     CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAG                         GATGCTCGTGTATGAGTATGTAGACAACGGCAATCTTGATCAATGGCTTCA
genomic: CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaa ... ggttgaacagGATGCTCGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTCA
EST: gi|58688663|gb|CK077350.1|CK077350
EST:     CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAG                         GATGCTCGTGTATGAGTATGTAGACAACGGCAATCTTGATCAATGGCTTCA
genomic: CATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaa ... ggttgaacagGATGCTCGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 50 (downstream exon)
Score: 8

AGGCTGAGAAGGAGTTCAAGGTGGAGGTTGAAGCGATCGGGCGTGTTCGGCATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCTTATAGgtacaatgaa ... ggttgaacagGATGCTCGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTCATGGTGATGTAGGGGAAGTGAGCCCACTAACTTGGGAAGTCAGGATGAAC




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