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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggtcaatagttggtacttagcagtaggcaacttataggttatgattcaagaagtccaacttttataaactgcagttaatgcatcatgtagaag...

Basic information

species Oryza sativa
transcript LOC_Os04g40874.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 7
CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggtcaatagttggtacttagcagtaggcaacttataggttatgattcaagaagtccaacttttataaactgcagttaatgcatcatgtagaag---
||||| ||||||||||||||||| || |||||||||||||||||||| |||||||||||||||||||||||||| | | || |||||| ||||||| || ||||| || || | | ||| | | ||||| |||||| | ||||| | |
CTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAGgtaagatcttttgtatttggtagctagcagttgggaacttc---attttgctggtataagctctatgcacataaattgcagtccctttatcattcaagaatgt

upper sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G22690.1 (Glycine max), 5'ss of exon 7
CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggtcaatagttggtact-tagcagtaggcaacttataggttatgattcaagaagtccaacttttataaactgcagttaatgcatcatgtagaag
| || ||||||||||| ||||| || ||| ||||||| |||||||||||||| |||| |||| | ||||| || || | | | | || || | | | | | ||| | | || | | | | || ||| |||| || |
TTAGTACTTCGTTTTGCAAACCGATTATTCATGCCTCTATGGAACCGTGACAACATTGCTAATGTGCAGgtgagaaagtgtgctgccaaagttactactgaagtcatcaaacaaggccttatt-agttggcttgacaaattcatatttcataatttgcctcatctaactg

upper sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 7
CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggtcaatagttggtacttagcagtaggcaacttataggttatgattcaagaagtccaacttttataaactgcagtta----atgcatcat--gtagaag---
| || ||||| ||||| || || || |||||||| ||||||||||| ||||| ||||| ||| ||||||| || ||| || | | | || ||||| | ||||| || | | | | ||| | || || ||| | | ||| | || ||
TTGGTACTTCGCTTTGCAAATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAATGTACAGgtgag------aatttttaattgtcaaagttaa--aactt-tgggttaagagttacttaaacttcatttatttaaatgaagtaagggaaggcactgttggttgagcttt

upper sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 5'ss of exon 7
CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggtcaatagttggtacttagcagtaggcaacttataggttatgattcaagaagtccaacttttataaactgcagttaatgcatcatgtagaag
| || || || ||||| || ||||| |||||||| |||||||||||||||||||| || || | ||||| || | | |||| | || || | ||| || | | ||||| || || || ||| ||| ||| || ||||
TTGGTCCTCCGGTTTGCAAATCGCTTTTTCTTGCCACTTTGGAACCGTGACAATATCGAGAACGTGCAGgtgaga-gctgcatagctaagac--agaaatagtcagactgtttgttat--ttagagtcaattcacattttcaaa-tgcttttcttgcag----------

upper sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 7
CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggtcaatagttggtacttagcagtagg--caacttataggttatgattcaagaagtccaacttttataaactgcagttaatgcatcatgtagaag-
| || ||||||||||| || ||| |||| ||||| || |||||||||||||| ||||||||| ||||||| || | || ||||| ||| | | | ||| ||| | || || ||| || | ||| | | || | | || |||
TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAGgttagattccttatt-ttggtgattacctctgaaacttatttacagggtgagac-catgaaagtaaattatta-actataagatttaggtggtatcctcaagt

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|29663317|gb|CB659592.1|CB659592
EST:     ACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG                         ATTGTATTCANGGGAG-ACTTTGGGACTGACGGGCGTGGTGGAT
genomic: ACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggt ... aatcctgcagATTGTATTCA-GGGAGGACTTTGGGACTGACGGGCGTGGTGGAT
EST: gi|86850539|gb|CI307768.1|CI307768
EST:     ACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG                         ATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGAT
genomic: ACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggt ... aatcctgcagATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGAT
EST: gi|88456177|gb|CI565827.1|CI565827
EST:     ACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAAT-T-GATAATATACAG                         ATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGAT
genomic: ACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggt ... aatcctgcagATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGAT

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: 69 (upstream exon), 59 (downstream exon)
Score: 64

CTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAGgtaagctggt ... aatcctgcagATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGATCAATATGG




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