Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAAGGATACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataatctctatgctatctaacacattcttactgttctatcttcttatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g46410.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g46410.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G132084_T04 (Zea mays), 5'ss of exon 9
GTTGCAAGGATACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataa-tctctatgctatctaacacattcttactgttctatcttcttatgcag
|| ||||||||| || ||||||| || ||||| || ||||| |||||||| |||||||||||| ||| || | |||| |  ||| ||||||      | | ||  |      | |  ||  | ||| ||||     |   ||  | |||   || |||| |   ||| |                  
GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATTTATTTGCATTACAGTCAGgtactaagatcttcattccaaatgaatttat------tctgtttaaaaaatatatactt-caagtataaatgtctttgtctcgttgtgccgcctgacacttaactacag------------------

upper sequence: LOC_Os03g46410.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G132084_T02 (Zea mays), 5'ss of exon 8
GTTGCAAGGATACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataa-tctctatgctatctaacacattcttactgttctatcttcttatgcag
|| ||||||||| || ||||||| || ||||| || ||||| |||||||| |||||||||||| ||| || | |||| |  ||| ||||||      | | ||  |      | |  ||  | ||| ||||     |   ||  | |||   || |||| |   ||| | |          ||||||
GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATTTATTTGCATTACAGTCAGgtactaagatcttcattccaaatgaatttat------tctgtttaaaaaatatatactt-caagtataaatgtctttgtctcgttgtgccgcctgacacttaactacagata---------atgcag

upper sequence: LOC_Os03g46410.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G016184_T02 (Zea mays), 5'ss of exon 8
GTTGCAAGGATACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataatctctatgctatctaacacattcttactgttctatcttcttatgcag
|| ||||||||| || ||||||| || ||||| || |||||||||||||| ||| |||||||| ||| || | |||| || ||||||||||      | | || ||     || |  | |  |||| |  ||       ||| | |||  ||| |||| |   ||| |                  
GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagatcttcattcctaatgcatttat------tctgttttacaaatttatagtcaactgtaaaggtatttgcc-tctttgtgccgtctgacacttaactacag------------------

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|33681072|gb|CF309311.1|CF309311
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|86852608|gb|CI321728.1|CI321728
EST:     GACTTCTGTTCAGGTACGTATTCTATCACATCTATATGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTAGTTGTGCCATC
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTA-TTGTGCCATC
EST: gi|86415587|gb|CI029598.1|CI029598
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|86261100|gb|CI004665.1|CI004665
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCAGTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|11025554|gb|AU162155.1|AU162155
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|86494039|gb|CI136672.1|CI136672
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|3763019|gb|AU029771.1|AU029771
EST:     CACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: CACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|89187704|gb|CI115150.1|CI115150
EST:     TCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
EST: gi|86259320|gb|CI007997.1|CI007997
EST:     TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAG                         GTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG
genomic: TACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCG

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: 66 (upstream exon), 28 (downstream exon)
Score: 7

GTTGCAAGGATACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacat ... tcttatgcagGTAATGCAGATGCATGCTTTTGGGTACTACTTGACATTTATTGTGCCATCGGTGCTCTTTGTCATGAACACAATGTGGTTTATGAAGATCTTGAAAGGCG




<











<


<