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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttcccaaatcttcatttctgtttactttggatttgagatggccctagtaactttatctgttatttatgcttgctcag

Basic information

species Oryza sativa
transcript LOC_Os04g55960.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G411448_T01 (Zea mays), 5'ss of exon 3
TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttcccaaatcttcatttctgtttactttggatttgagatggccctagt--aactttatctgttatttatgcttgctcag---
|||||| ||||||||||| ||||| ||||| |||||| ||||||| |||||||||||||||||||| |||||| | || || |||||||||||||||||||||||||| || | |      |   ||| || ||   |       ||    ||||  |||||  |||   | |    |   |   |   
TGTGAGACAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgtttcccaagaatccagtgggtgtgtatttgcaaggctgcttgagagtagtttaacttattcttgcactccctccctcctggcag

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G377451_T01 (Zea mays), 5'ss of exon 11
TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttcccaaatcttcatttctgtttactttggatttgagatggccctagt--aactttatctgttatttatgcttgctcag---
|||||||||||||||||| ||||| ||||  |||||| ||||||| |||||||||||||||||||| |||||| | || || ||||||||||||||||||||||||||||| | |      |   | | || ||   |       ||    ||||  |||||  ||    | |    |   |   |   
TGTGAGGCAGTCAAATTTCAAGTTACCTGATGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttccaagaatccagtgggtctgtatttgcaaggctgcttgagagtagtttaacttattcctgcactccctccctcctggcag

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G086489_T01 (Zea mays), 5'ss of exon 14
TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttcccaaatcttcatttctgtttactttggatttgagatggccctagt--aactttatctgttatttatgcttgctcag---
|||||||||||||||||| ||||| ||||| |||||| ||||||| |||||||||||||||||||| |||||| | || || ||||||||||||||||||||||||||||| | |      |   ||| || ||   |       ||    ||||  |||||  |||   | |    |   |   |   
TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttccaagaatccagtgggtgtgtatttgcaaggctgcttgagagtagtttaacttattcttgcactccctccctcctggcag

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G480134_T01 (Zea mays), 5'ss of exon 4
TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttcccaaatcttcatttctgtttactttggatttgagatggccctagt--aactttatctgttatttatgcttgctcag---
|||||||||||||||||| ||||| ||||  |||||| ||||||| |||||||||||||||||||| |||| | | || || ||||||||||||||||||||||||||||| | |     ||   ||| || ||   |       ||    ||||  |||||  |||   | |    |   |   |   
TGTGAGGCAGTCAAATTTCAAGTTACCTGATGATCCGTCCACTCCTATTATCATGATTGGTCCTGGGACAGAGCTGGCTCCTTTTAGAGGCTTCTTGCAGgtttgttttccaagaatccaatgggtgtgtatttgcaaggctgcttgagagtagtttaacttattcttgcactccctccctcctggcag

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 8
TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttcccaaatcttc--atttctgtttactttggatttgagatggccctagtaactttatctgttatttatgcttgctcag-------
|||||||||||||||||| ||||| ||||| || ||  ||||||| |||||||||||||||||||| |||||| | || || |||||||| ||||||||||||||||||  |||    ||  ||   ||| || ||    ||     ||     |   |  ||| ||  |  ||  |||  |||         
TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttggcaaggagtccaatgggtgtatatttgcagttctgcttgagagcacctagcttaacttatccttccgctctctctattggcag

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|27577335|gb|CB000030.1|CB000030
EST:     TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAG                         GAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
genomic: TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttc ... gcttgctcagGAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
EST: gi|58666486|gb|CK055172.1|CK055172
EST:     TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAG                         GAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
genomic: TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttc ... gcttgctcagGAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
EST: gi|163926612|gb|EG713628.1|EG713628
EST:     TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAG                         GAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAATTCTC
genomic: TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttc ... gcttgctcagGAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
EST: gi|163929241|gb|EG712694.1|EG712694
EST:     TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAG                         GAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
genomic: TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttc ... gcttgctcagGAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
EST: gi|58681936|gb|CK070623.1|CK070623
EST:     TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAG                         GAAAGATTAGCTCTAAAAC
genomic: TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttc ... gcttgctcagGAAAGATTAGCTCTAAAAC
EST: gi|58673422|gb|CK062108.1|CK062108
EST:     TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAG                         GAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
genomic: TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttc ... gcttgctcagGAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
EST: gi|27576047|gb|CA998741.1|CA998741
EST:     TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAG                         GAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC
genomic: TCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttc ... gcttgctcagGAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTC

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: 72 (upstream exon), 73 (downstream exon)
Score: 50

TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttc ... gcttgctcagGAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTCTTCTTTGGATGCAGGAACCGTAATATG




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