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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttcctgttggaggaaaactattctgtgttttttgcatttgtcttggttgtacattcatttatttcgtgttggtcattattattgcttttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTA

Basic information

species Oryza sativa
transcript LOC_Os05g01450.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01450.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G098153_T01 (Zea mays), 3'ss of exon 3
---------ttatttcctgttggaggaaaactattctgtgttttttgcatttgtcttggttgtacattcatttatttcgtgttggtcattattattgcttttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTA
          ||  | ||||| |   | ||| ||  |    | |   || || |  | |  | |||||  |  |  |    |   || ||| |||  ||||||  |||||||| |||||||||||||| || || |||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||  | |||||||| ||||||||
ttctcgcaaatagctgctgtttgtt-agaaccataatacagtct---caattttagtagcagaacatt--tcaaacttccatcactc-ttactat--cttttggtacagTTGAGATCCTGAAATCTACGATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCCTCAATGGAGAAGCTTTACATTCTTATTGATGAGATCTA

upper sequence: LOC_Os05g01450.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G025214_T02 (Zea mays), 3'ss of exon 8
--ttatttcctgttggaggaaaactattctgtgttttttgcatttgtcttggttgtacattcatttatttcgtgttggtcattattattgcttt-tgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTA
   |  |   |||  ||   | | | | || || |   | | |  || || || | | |  ||||| |   |  |   ||| | ||| | | || ||| |||||||| |||||||||||||| || || |||||||||||||||||||||||||||||||| || || ||||  ||||| ||  | ||||| || ||||||||
aactgatgtttgtaagaaccatattttgctctgctacat-cctcagttttagtagcagaa-cattt-tgaagcttccatcactcttactaccttctgttacagTTGAGATCCTGAAATCTACTATGGTAGAGAAGCTCCCCAATGATCTGGAAGGAATGGAGTCATCGATGGGGAAGCTTTACATTCTTATCGATGAGATCTA
















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|87013558|gb|CI267259.1|CI267259
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|25807581|gb|CA763542.1|CA763542
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|58595951|gb|CK006479.1|CK006479
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|58598359|gb|CK008887.1|CK008887
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|2431154|gb|C73574.1|C73574
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|88846943|gb|CI005922.1|CI005922
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|3760827|gb|C98081.1|C98081
EST:     GGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: GGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|88223674|gb|CI223523.1|CI223523
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|33803402|gb|CF327575.1|CF327575
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGGAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|88210483|gb|CI210332.1|CI210332
EST:     GATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: GATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|86495486|gb|CI138119.1|CI138119
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|88507869|gb|CI435375.1|CI435375
EST:     CTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|88985008|gb|CI011864.1|CI011864
EST:     AGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: AGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|117237389|gb|CT861885.1|CT861885
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|33689596|gb|CF317835.1|CF317835
EST:     CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAACAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: CCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
EST: gi|88262599|gb|CI366373.1|CI366373
EST:     TGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACGATTGTGGAGAAGCTCCCCAATGATGCTGGAA
genomic: TGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGAT-CTGGAA
EST: gi|86259276|gb|CI007953.1|CI007953
EST:     AGGATGCTTGAAGCAGGAAAAGTTGGAT                         TTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG
genomic: AGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAG

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: 74 (upstream exon), 73 (downstream exon)
Score: 34

TATATCTCATCCAACCTGTCTCTTGGAGATAGGCACCTTGCTGCGCAGTTCCAAGAGATTCCCCTTGATCTGAGGATGCTTGAAGCAGGAAAAGTTGGATgtatgtctca ... tttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggttgtacattcatttatttcgtgttggtcattattattgcttttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTA
                                        ttgctttt  CT-rich tract
        tacattcatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttcctgttggaggaaaactattctgtgttttttgcatttgtcttggttgtacattcatttatttcgtgttggtcattattattgcttttgtgacagTTGACATCCTGAAATCTACAATTGTGGAGAAGCTCCCCAATGATCTGGAAGGAATGGAATCCTCCATGGAAAAGCTGTATGTCCTTATTGACGAGATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC