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'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCCCAATTTAGATATCTTGGAGATGTTTCGATTCCCTTCGCTACAGGTGCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatcaatcttttatgtgcagttatttattcccacactaagttttctttctttctatttttgctttgtgatttcccatgtcgtaatcttgtgttc...

Basic information

species Oryza sativa
transcript LOC_Os01g46510.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46510.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM5G824843_T01 (Zea mays), 5'ss of exon 2
GGCCCCAATTTAGATATCTTGGAGATGTTTCGATTCCCTTCGCTACAGGTGCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatcaatcttttatgtgcagttatttattcccacactaagttttctttctttctatttttgctttgtgatttcccatgtcgtaatcttgtgttc--
||||||||||||| || |||||||||||||| |||||||| || || ||||||||||||||||| |||||||| |||||| |||| || || || || |||||||   | |||||| | | | |    ||    | |  |  |     ||         ||| |     |||  ||     |||| | || ||||| |    
GGCCCCAATTTAGGTACCTTGGAGATGTTTCAATTCCCTTTGCAACTGGTGCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagattttaatcttctttatacttcaatgatgttcggctttttcccttgaaagaagatatctcaatattgctatgatt-atgt-gcaagcttgtatatag

upper sequence: LOC_Os01g46510.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT5G24710.1 (Arabidopsis thaliana), 5'ss of exon 14
GGCCCCAATTTAGATATCTTGGAGATGTTTCGATTCCCTTCGCTACAGGTGCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagc-catcaatcttt-tatgtgcagttatttattcccacacta----agttttctttctttctatttttgctttgtgatttcccatgtcgtaatcttgtgttc
| || || | |||||||||||| |||||| | ||| |    ||||| || || ||||||||||| || ||| ||||||||||||| || ||||| || ||||||||  ||   ||| | ||||     | |||| || |     |     ||||  |||   | ||| ||   |||   |||    ||      ||  |       
GCCCTCAGTATAGATATCTTGGTGATGTTGCCATTGCACATGCTACTGGAGCTGTTTGGCATCGCAGACAGCTGTTTGTGGCTACACCAACCACGATTGAgtaagcatattgctctatatatgatacatgatttttttctgtcttctgccagttaccttaaatgctacttccacttg--gatgaaacaaactaaaaattgaa----

upper sequence: LOC_Os01g46510.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv08s0056g00040.t01 (Vitis vinifera), 5'ss of exon 15
GGCCCCAATTTAGATATCTTGGAGATGTTTCGATTCCCTTCGCTACAGGTGCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatcaatcttttatgtgcagttatttattcccacactaagttttctttctttctatttttgctttgtgatttcccatgtcgtaatcttgtgttc-
| || |||| ||||||  | ||||||||  | |||||||  ||||| ||||| |||||||| || || ||| ||||||||||||| || || ||||| |||||||  || | |   | |   |||    ||   |       |||    | |    |    ||| ||   ||| |||        |  | | |  |  |  
GCCCTCAATATAGATACTTGGGAGATGTGGCCATTCCCTATGCTACTGGTGCTGTTTGGCACCGGAGACAGCTGTTTGTGGCTACACCAACTACCATTGAgtaagttat-agttgatgaccagcaacacttctgtttttagttaaccaatttggagtgaactttatgtgatgttattctttgcaactcattttgttaatag

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|58662672|gb|CK051358.1|CK051358
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGACATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58664662|gb|CK053348.1|CK053348
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58666107|gb|CK054793.1|CK054793
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58666827|gb|CK055513.1|CK055513
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58665271|gb|CK053957.1|CK053957
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58587152|gb|CF985460.1|CF985460
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58612809|gb|CK040521.1|CK040521
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58612142|gb|CK039854.1|CK039854
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTGTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|86889062|gb|CI314678.1|CI314678
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTG
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTG
EST: gi|25804329|gb|CA760290.1|CA760290
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAAC
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAAC
EST: gi|58662716|gb|CK051402.1|CK051402
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58666361|gb|CK055047.1|CK055047
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAA
EST: gi|88399115|gb|CI603782.1|CI603782
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCAC-ACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
EST: gi|58669479|gb|CK058165.1|CK058165
EST:     GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGA                         GTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA
genomic: GCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAA

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: 65 (upstream exon), 74 (downstream exon)
Score: 32

GGCCCCAATTTAGATATCTTGGAGATGTTTCGATTCCCTTCGCTACAGGTGCCGTTTGGCATCGTAGGCAGTTGTTTGTGGCTACGCCCACCACCATCGAgtaagccatc ... taatatccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAAGAGGAAAGAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCGGCTGCA




<











<


<