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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATGCTGCTGCTAGACCTGTAATATTGGAACCAGTGATGAAAGTGGAACTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgtttgatcgtaactttgcttctactgaaatgtatggttacacactcttaatcagtttcatgtgaagtgttccttttgggttcaagttaatattt...

Basic information

species Oryza sativa
transcript LOC_Os03g36780.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 17
GTTATGCTGCTGCTAGACCTGTAATATTGGAACCAGTGATGAAAGTGGAACTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgtttgatcgtaac----tttgcttctactgaaatgtatggttacacactcttaatcagtttcatgtgaagtgttccttttgggttcaagttaatattt
| ||  || |||| | |||||||||||| ||||| |||||||| |||||||| ||| |||| || ||||| |||||||| ||||| ||||| |||||||||| |||| ||  |   |||    | | | |||| || ||  |||||    |    | | ||   |||||||   ||  ||| ||||    |||||  |||    
GCTACACTTCTGCCAAACCTGTAATATTAGAACCTGTGATGAAGGTGGAACTCAAATTTCCAACTGAGTTTCAGGGCACAGTAACTGGTGATATGAACAAgtaagtgctttgttccaacaagttatccctctattgtaaattatggccgga---acatcatttatttcatgcatagaattctttttcttctcaaga-aatgccg
















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|89187096|gb|CI047163.1|CI047163
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|89164137|gb|CI101225.1|CI101225
EST:     CTAAAAGTTCCCACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|87027719|gb|CI274283.1|CI274283
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|86434221|gb|CI094564.1|CI094564
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|29670886|gb|CB667161.1|CB667161
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|86849356|gb|CI297811.1|CI297811
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|89192591|gb|CI049889.1|CI049889
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|88965002|gb|CI097870.1|CI097870
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|88966342|gb|CI119477.1|CI119477
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|86255945|gb|CI068394.1|CI068394
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|87023356|gb|CI272184.1|CI272184
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
EST: gi|58693580|gb|CK082267.1|CK082267
EST:     CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAA                         GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT
genomic: CTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGT

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), 46 (downstream exon)
Score: 30

GTTATGCTGCTGCTAGACCTGTAATATTGGAACCAGTGATGAAAGTGGAACTAAAAGTTCCTACAGAGTTCCAGGGCACGGTAACCGGTGACATGAACAAgtgagtgttt ... tggaaaacagGAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT




<











<


<