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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccgcctcgccccccgattcattcatccatccatccattcattgacggcgagtttgctccttctttcattagtccgatccgttcttgattagcg...

Basic information

species Oryza sativa
transcript LOC_Os07g26940.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26940.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G044720_T01 (Zea mays), 5'ss of exon 1
CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccgcctcgccccccgattcattcatccatccatccattcattgacggcgagtttgctcctt--ctttcattagtccgatccgttcttgatta-gcg---
|||||||||||| ||||||||||| ||||| ||||||||||||||||| |  |||||||||||    || ||||| ||||| |||||||| |||||||||||  || ||    | ||| |  ||||  ||  |  ||| ||      |  || | | |||||||      |  |   | |  |||||   |  |||||  |||   
CTACATCCTCCTGCTCTTCTTCGCTTGGCTCCTCGTCCTCTCCGTCTCTGGTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttcc----caccctct-attccgtccccagtccctcgccctttctactg-gggtttgcttacgagcggttgctcgcgcgatcgacttctgattttgcgcat

upper sequence: LOC_Os07g26940.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G064898_T02 (Zea mays), 5'ss of exon 1
CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccgcctcgccccccgattcattcatccatccatccattcattgacggcgagtttgctcctt-ctttcattagtccgatccgtt--cttgattagcg
|||||||||| | ||||||||||||||||| ||||||||||||||||| |  |||||||| |||   || |||||||||||||||||||| |||||||||||  |||||  | | |   |   | |     ||| ||   |   | |||    ||  || |     |  ||| | |       |||| |    ||| ||    
CTACATCCTCATGCTCTTCTTCGCCTGGCTTCTCGTCCTCTCCGTCTCTGGTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCCgtgagtccccaccctctatctcgtcc-ccagtccctcgcccttctgattttgcgcatgtctatggatcgcttccgtccactgtatccctagatttggttgt--

upper sequence: LOC_Os07g26940.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G05940.1 (Glycine max), 5'ss of exon 1
CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccgcctcgcccccc--gattcattcatccatcca--tccattcattgacggcgagtttgctccttctttcattagtccgatccgttcttgattagcg
 ||||||||| |||| |||||  | ||| | ||||| |||||||||| ||  ||||||||||| ||||| |||||| |||| || ||||| ||||| || |||  || | | |    ||     |||  ||| |   | ||  |  |   |||||    |||||       ||||| |||  |    |  ||  ||   |    
TTACATCCTCATCCTTTTCTTTTCTTGGATCCTCGTTCTCTCCGTCTTCGGTTGCTCCCCCGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatctctctctttcttccttttaattatttcctttttacaaataaaaaaattgaaattgagttctgggtgtctttgattttttgatttggtgatttggt----

upper sequence: LOC_Os07g26940.3 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 5'ss of exon 1
CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccgcctcgccccccgattcattcatccatccatccattcattgacggcgagtttgctccttctttcattag--tccgatccgttcttgattagcg
|||||||||| | ||||||||||| ||||| || || |||||| ||| || |||||| || || || |||||||| |||||||| |||  ||||||    ||| ||      ||          ||    ||       |   ||  ||    |    |||| |   | ||  | |    | || |   ||  |||||    
CTACATCCTCATTCTCTTCTTCGCATGGCTCCTTGTTCTCTCCATCTTCGGCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtttttcttttgatttctctcagattttgggtttttttttttttttgtttttttgttgagttttcaagtgtgtttcggttatttgatgatttt--

upper sequence: LOC_Os07g26940.3 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S123_9V6.1 (Physcomitrella patens), 5'ss of exon 1
CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccgcctcgccccccgattcattcatccatccatccattcattgacggcgagtttgctcct-tctttcattagtccgatccgttcttgattagcg-----
 || || ||  |  |||| ||| | |||||   | || ||||||  | |   |||    |||| | ||| ||||| ||||||||||||| |||||||||||||     ||| ||  || | | ||| |   |   |   |   ||    || || |||||||    | |  ||     |   |    | | ||| |   |      
GTATATTCTGATTATCTTGTTCTCGTGGCTCGCCATCGTCTCCGCGTTCCGATGCGATGCCGGAACCGCATGGACTGTCGTCAACCTCGTCCACTTCGCCgtaa----cgcgtc-tcctctgtttcttcgttgtgtatctttgtt-gcggatggggagtttgtaggtgtgatttgagggatgggagtgcttttgctaccccttcgt

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|58589386|gb|CF987694.1|CF987694
EST:     CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCC                         ATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
genomic: CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccg ... tttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
EST: gi|218487860|gb|FG958482.1|FG958482
EST:     CTGCTCCCCCTGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCC                         ATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
genomic: CTGCTCCCCC-GGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccg ... tttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
EST: gi|14714226|gb|AU198157.1|AU198157
EST:     CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCC                         ATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
genomic: CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccg ... tttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
EST: gi|7273842|gb|AU083386.1|AU083386
EST:     CCTGTTCCCCNGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCC                         ATCACTTATCACTTCTTCCCATTGGAAGAAGGGAACTCCATTTGCTGCTGA
genomic: CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccg ... tttttggcagATCACTTATCACTTCTT-CCATTGGAAGAAGGGAACTCCATTTGCTGCTGA
EST: gi|58688367|gb|CK077054.1|CK077054
EST:     CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCC                         ATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT
genomic: CCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccg ... tttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGAT

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: 74 (upstream exon), 67 (downstream exon)
Score: 69

CTACATCCTCCTCCTCTTCTTCGCCTGGCTGCTCGTCCTCTCCGTCTCCGCCTGCTCCCCCGGGATCGCGTGGACCGTCGTCAACCTCGCCCACTTCGCCgtacgtcccg ... tttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG




<











<


<