Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG

Basic information

species Oryza sativa
transcript LOC_Os01g64650.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 1
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgtt-gttaatgaacggtcatgtaa-acaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
 ||      | | ||  | | || | | | | |||  |||  |     |||| |||   ||   | | | |  | | | | |   | || |   |||| ||||||| ||||| ||||| |||||||| ||||| ||||| || || ||||||||||||||||||||||||||||||||||||||||||||||||||| ||
cataacatatggctgaccctgtttgctttggagatttggaatacatt-tttgttgtccatttccgcatgctgttttgacatacaatctcttcccattt-cagAATATAAGGTTCACTCCCACAACAGAAATGGGCTTTGTGCGGTGGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G446711_T01 (Zea mays), 3'ss of exon 1
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgtt-gttaatgaacggtcatgtaa-acaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
|        | | ||  | | || | | ||| |||   ||  | |   |||||| ||  ||      || |  ||| |   |   | || |   |||| ||||||||||||||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||||||||||  ||||||||||||||||||||| ||
ataacattatggctggccctgtttgctttagagatattgaatacttt-tttgctattcatttccactcgctgttgtgacgtacaatctcttttcattt-cagAATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCAGTTGCATTCATGGATGATCATTATCCTGTACAGAGTGCATTTTCTCTTCTGAATCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 2
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgtt-gttaatgaacggtcatgtaa-acaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
|        | | ||  | | || | | ||| |||  |||  |     |||||||||  ||      || |  ||| |   |   |||| |   |||| ||||||||||||||||||| ||||| || ||||| ||||| || |||||||| ||||||||||| ||||| ||||| ||||||||||||||||||||| ||
ataacattatggctgaccctgtttgctttagagatatggaatacatt-tttgctgttcatttccactcgctgttgtgacgtacaatgtcttttcattt-cagAATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
|   |    |   | || || |  |||    |  |        |  ||| | |  |   |  |         |||||     ||    |  | | |||||| |||||||| ||| || ||||||| ||||||||||||||  | | ||||||||||||||| || ||  | || ||||| ||||||||||| ||  ||
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctgtgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 1
aatctgcagtcgatgtt-cattttcggtctagtgatcaggagaattcagtttgc----tgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
       |  || | |   || || | | |   | |  |     ||    ||||    |  ||| | |       | | |  |    ||    | || |||||||| |||||||| ||| || ||||||||||||||||||||||  | | ||||||||||||||| || ||  | || ||||| ||||||||||| ||| ||
-----ataaccgttttgatatcttggttttgccggttcgatttctttttgttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 1
----aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtca-tgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
      | | | || ||   || ||||   | |  ||||  |      | |   || | |  ||  | || | | | | |      || |   | ||||    |||||| || || || ||  ||||||| ||||||||||| ||| | |  ||||||||||| ||||||||||| ||||| ||||||||  | || ||  ||
gttttgtttcctgtggaaagtc-ttttgtatgttttgatatgttattgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatat----agAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG

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|218482998|gb|FG956126.1|FG956126
EST:     CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
EST: gi|88573365|gb|CI664936.1|CI664936
EST:     GTCGCCCAGCCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: GTCGCCCAGC-GCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
EST: gi|4879970|gb|AU064269.1|AU064269
EST:     CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTTGCGCATTTGCATTT
genomic: CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTT-GCGCAGTTGCATTT
EST: gi|38468730|gb|CF952861.1|CF952861
EST:     GGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: GGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
EST: gi|88243877|gb|CI242999.1|CI242999
EST:     CGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: CGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
EST: gi|218479888|gb|FG958307.1|FG958307
EST:     CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
EST: gi|27578119|gb|CB000814.1|CB000814
EST:     CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA

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: 68 (upstream exon), 74 (downstream exon)
Score: 21

TTCTTCCAGCGGGGCGCCGCGCGGGAGTTCATCGTCTTCGTCGCGCGCACCGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttgctgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
                                        tcctgat  putative branch site (score: 21)
          ttgttaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG

-atctgca
- - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa