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

GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctatagcttcagtccttttgttcagcactcagttcacttatcagttgaatatccgagcttgcataaagactctaatcagaacattttattgatag

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G030902_T02 (Zea mays), 5'ss of exon 6
GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctatagcttcagt-ccttttgttcagcactcagttcacttatcagttgaatatccgagcttgcataaagactctaatcagaacattttattgatag
||||||||||||||||| ||| |||| || ||||| || |||||||||||||||||||| ||||| ||||| ||||| ||||||||||||| ||||| || || | | |||||| ||||  |   |  || ||              | | |||||  ||||           ||    |||| | | ||
GAAGAAATGAAATCACAAGGAACAAAGAAAGCTACAAGGATATTTGTTGCTCGAATTCCACAGTCAGTGGACGAGTCGATGTTTCGTAGgtcagctagaggtttactgccttttcttcattatctatatcccta-------------ctgggcttgtttaaa--------ctggattgctttactaacag

upper sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G060977_T01 (Zea mays), 5'ss of exon 6
GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctatagcttcagtccttttgttcagcactcagttcacttatcagttgaatatccgagcttgcataaagactctaatcagaacattttattgatag
||||||||||||||||| |||||||| || ||||| || ||||| ||||||||||||||||| || ||||||||||| ||||||||||||| || || ||| |   | ||||| ||||  |   |  || |||||   ||   |||| |||||||  ||||           ||  | |||||| | ||
GAAGAAATGAAATCACAAGGATCAAAGAAAGCTACAAGGATATTCGTTGCTCGAATTCCGCAATCGGTGGATGAGTCGATGTTTCGTAGgtcagttagagcatttatactttttttcattatctatatc-cttattgatttg-tatc-gagcttgtctaaa--------ctggactactttattaacag
















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|117251528|gb|CT844202.1|CT844202
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
EST: gi|33682634|gb|CF310873.1|CF310873
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATG
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATG
EST: gi|58598133|gb|CK008661.1|CK008661
EST:     ATATTGGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
EST: gi|32947891|gb|BP184463.1|BP184463
EST:     GAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
genomic: GAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
EST: gi|58603513|gb|CK014041.1|CK014041
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGGGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
EST: gi|58676983|gb|CK065670.1|CK065670
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTACATGTTTCGTAG                         GCCTTTTGAAGCCTATGGAGAAATCACTGATCTTTACAT
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACAT
EST: gi|29677102|gb|CB673377.1|CB673377
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
EST: gi|116875665|gb|EC366173.1|EC366173
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
EST: gi|58591906|gb|CF990214.1|CF990214
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGC
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGC
EST: gi|33800393|gb|CF326065.1|CF326065
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTCGAAGCCTATGGAGAAATCACTGATCTTTACATGCC
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCC
EST: gi|116875549|gb|EC366057.1|EC366057
EST:     CTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
genomic: CTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
EST: gi|33684319|gb|CF312558.1|CF312558
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG
EST: gi|86596647|gb|CI286560.1|CI286560
EST:     ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAG                         GCATTTTGAAGCCTATGGAGAAATCACTGATC
genomic: ATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATC

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), 55 (downstream exon)
Score: 34

GAAGAAATGAAATCACAGGGATCAAAAAAGGCTACTAGAATATTTGTTGCTCGAATTCCGCAGTCCGTGGATGAGTCCATGTTTCGTAGgtaagctata ... ttattgatagGCATTTTGAAGCCTATGGAGAAATCACTGATCTTTACATGCCAAAG




<











<


<