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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtaactgctttctcttactattttctgttaacttttagcaaaaaagaatgaatagtgagagttttctctgactattttctgttaattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAATGCGTGAATTTCGAGTTAATTCGGTGGTTGTTGCTACAGGAAACACACTA

Basic information

species Oryza sativa
transcript LOC_Os12g07190.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 5
gtacagtaactgctttctcttactattttctgttaacttttagcaaaaaagaatgaatagtgagagttttctctgactattttctgttaattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAATGCGTGAATTTCGAGTTAATTCGGTGGTTGTTGCTACAGGAAACACACTA
||| || |     ||| |   |||||||||| | || | |||||||   ||||  || | | ||        || |||||     | ||  || ||| |||||||||||||| ||| |||| || |||| ||||||| |||| |||||||| || ||| | |||||||| ||||||||  |||||||||||||| | 
gtatagcattgattttgttggactattttctttcaattgttagcaat--agaaacaacatttag--------ctaactat-----gctatcttgcagAGTAGCAATTGTTTCGCCTACAGATCCTGTGTGTGTAGCAGCACAAAAAATGCGAGAGTTTTGTGTTAATTCAGTGGTTGTCTCTACAGGAAACACATTG
















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|29616351|gb|CB621363.1|CB621363
EST:     GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAA                         GGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
genomic: GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAAgtacagtaac ... taattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
EST: gi|29658205|gb|CB654480.1|CB654480
EST:     GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAA                         GGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
genomic: GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAAgtacagtaac ... taattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
EST: gi|58612797|gb|CK040509.1|CK040509
EST:     GAGAGGATGTTCAAACCTTCTTTGTCAAGCATTGTCACGGAGGGCACAAA                         GGTAGCAATAGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
genomic: GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAAgtacagtaac ... taattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
EST: gi|29620736|gb|CB625747.1|CB625747
EST:     GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAA                         GGTAGCAATTGTTTCTCCT
genomic: GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAAgtacagtaac ... taattttcagGGTAGCAATTGTTTCTCCT
EST: gi|29683887|gb|CB680162.1|CB680162
EST:     GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAA                         GGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
genomic: GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAAgtacagtaac ... taattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
EST: gi|58693946|gb|CK082633.1|CK082633
EST:     GAGAGGATGTTCAAACCTTCTTTGTCAAGCATTGTCACGGAGGGCACAAA                         GGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
genomic: GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAAgtacagtaac ... taattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
EST: gi|29617498|gb|CB622510.1|CB622510
EST:     GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAA                         GGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT
genomic: GAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAAgtacagtaac ... taattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAAT

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: 62 (upstream exon), 59 (downstream exon)
Score: 32

CTCCTTATGCTTTCATAGAAACTCTAAGAGAGAGGATGTTCAAACCTTCTTTGTCAACCATTGTCACGGAGGGCACAAAgtacagtaac ... taattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAATGCGTGAATTTCGAGTTAATTCGGTGGTTGTTGCTACAGGAAACACACTA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaaaaagaatgaatagtgagagttttctctgactattttctgttaattttcagGGTAGCAATTGTTTCTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAATGCGTGAATTTCGAGTTAATTCGGTGGTTGTTGCTACAGGAAACACACTA
                                          tgttaat  putative branch site (score: 32)
                                     ttttctgtt  CT-rich tract
                                   tattttctgttaattt  TA-rich tract