Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCAGTGGATCCGTGTAGCAGTGAAGAAAGGGGGCATGATTGTTTTGCCTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttgctttgttcctttgttcccacaaatagttatgttataagcatcaaactgactttgacgtgaacttatgcgttttaagtatattggtgaaca...

Basic information

species Oryza sativa
transcript LOC_Os03g06620.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06620.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G165998_T01 (Zea mays), 5'ss of exon 5
TGATCAGTGGATCCGTGTAGCAGTGAAGAAAGGGGGCATGATTGTTTTGCCTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttgctttgttcctttgttcccacaaatagttatgttataagca--tcaaactgactttgacgtga-acttatgcgttttaagtatattggtgaaca
||||||||||||||||||||| || ||||||||||||||||| ||||||||||| ||||||||||| ||||| || ||||| ||||||||||||||||||||||||||  |||  || || ||||| ||| |  |||| |||| |    |  ||         ||||   ||   | || | ||||   | |   |  |    
TGATCAGTGGATCCGTGTAGCGGTAAAGAAAGGGGGCATGATCGTTTTGCCTGCAGGAATGTATCATCGCTTTACGTTGGATAGTGACAACTACATCAAGgtatctttgacttc-tttctctgttcacactatgagttttgttctttttaactctggtaattgttgattagatgatgataccttttctttgtgaagccgtt--

upper sequence: LOC_Os03g06620.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0020g04080.t01 (Vitis vinifera), 5'ss of exon 5
TGATCAGTGGATCCGTGTAGCAGTGAAGAAAGGGGGCATGATTGTTTTGCCTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttt-tgctttgttcctttgttcccacaaatagttatgt-tataagcatcaa-actgactttgacgtgaacttatgcgttttaagtatattggtgaaca
|||    |||||||||||     | |||||||| || |||||||| || ||||| ||||| |||||||| |||||| ||||     ||||||||||||||||| ||||   ||   | | | ||   |   || ||||  | | | |      ||| | || |  | |    | |     |  |   | |||||     |   
TGACTCTTGGATCCGTGTGTGGCTAAAGAAAGGAGGAATGATTGTATTACCTGCTGGAATTTATCACCGGTTCACACTGGATTCGAACAACTACATCAAGgtagctttacactccatgcttatgaaacacaaattagtggtttgtttgcctgccaagaatggcaataataataccaataccactaggactatatattcta---
















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|88960442|gb|CI006403.1|CI006403
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|86525921|gb|CI166127.1|CI166127
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|58594368|gb|CF992676.1|CF992676
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|88514217|gb|CI441723.1|CI441723
EST:     CAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|23514051|gb|BU673448.1|BU673448
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|88841102|gb|CI001064.1|CI001064
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|58591300|gb|CF989608.1|CF989608
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|313084041|gb|HO213824.1|HO213824
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGT
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGT
EST: gi|88995973|gb|CI037264.1|CI037264
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|33662546|gb|CF293513.1|CF293513
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGG
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGG
EST: gi|117246064|gb|CT862529.1|CT862529
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|89195617|gb|CI393646.1|CI393646
EST:     CACATT-GACAGTGACAAGTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|33659101|gb|CF281714.1|CF281714
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|86825253|gb|CI359939.1|CI359939
EST:     CGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGC-GCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|89175794|gb|CI042815.1|CI042815
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|8858785|gb|AU096103.1|AU096103
EST:     CTGCGGGAATGTATCNCCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|88519132|gb|CI446786.1|CI446786
EST:     GACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: GACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|33659100|gb|CF281713.1|CF281713
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|46573741|gb|CN487723.1|CN487723
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCA-TGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|86596709|gb|CI286622.1|CI286622
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|88268616|gb|CI378551.1|CI378551
EST:     ATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: ATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|218494503|gb|FG957959.1|FG957959
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|86866329|gb|CI336941.1|CI336941
EST:     CATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
genomic: CATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCC
EST: gi|58587763|gb|CF986071.1|CF986071
EST:     CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAG                         GCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCC
EST: gi|88445319|gb|CI587213.1|CI587213
EST:     CTGCGGGAATGTATCACCGCTT-ACATTGGACAGTGACAACTACATCAAG                         -CA-TGCGGTTTTTTGTGGGAAAGCCTGT-TG-AC-CCGTACA-CCGTCC
genomic: CTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCC

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), 71 (downstream exon)
Score: 115

TGATCAGTGGATCCGTGTAGCAGTGAAGAAAGGGGGCATGATTGTTTTGCCTGCGGGAATGTATCACCGCTTCACATTGGACAGTGACAACTACATCAAGgtatcttttg ... gcttctgcagGCAATGCGGCTCTTTGTGGGAGAGCCTGTCTGGACGCCGTACAACCGTCCCCATGACCATCTGCCAGCTAG




<











<


<