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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaggtccacctgctttcttgatgttgtaccatcactgttttgctgattgttgttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGTGGTTACCGTGGCGGCGGTCGCGCCCGTGGGTCATACTACGGTGGCAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g02090.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 7
-----gtacaaggtccacctgctttcttga-tgttgtaccatcactgttttgctgattgttgttt-tgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGTGGTTACCGTGGCGGCGGTCGCGCCCGTGGGTCATACTACGGTGGCAGAG
     | || |   ||||||   |||| || | ||  ||  |  ||| |||||| |||||| ||  ||||||||| ||||| || || || |||||  | |||||||| |||||||| || || || ||||||||||| || ||  ||||||| ||||| |||||||||||||
gtactggaccaaaaccacctttcttctcgagttttccactgttgctgctttgctcattgttattggtgtgcagACGTTTGGCGAATTTCCGAGGCACAGGCAGCCCTACCGTGGTGGCGGCCGAGGCTACCGTGGCGGTGGGCGTTCCCGTGGTTCATATTACGGTGGCAGAG
















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|29670874|gb|CB667149.1|CB667149
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|86437498|gb|CI119220.1|CI119220
EST:     GGCAAAACGGGAGGTCAAGACTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|29670778|gb|CB667053.1|CB667053
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|8857577|gb|AU094895.1|AU094895
EST:     GCAAAACGGGAGGTCCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GCAAAACGGGAGGT-CAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|29636684|gb|CB641693.1|CB641693
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|29668187|gb|CB664462.1|CB664462
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|29668186|gb|CB664461.1|CB664461
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|29626801|gb|CB631812.1|CB631812
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|29631207|gb|CB636216.1|CB636216
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|29668147|gb|CB664422.1|CB664422
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|88675876|gb|CI729448.1|CI729448
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|8856551|gb|AU093869.1|AU093869
EST:     AAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: AAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|88673022|gb|CI727137.1|CI727137
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATANAGAG                         ACCTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCG
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagAC-TTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCG
EST: gi|29668148|gb|CB664423.1|CB664423
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
EST: gi|29638812|gb|CB643821.1|CB643821
EST:     GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAG                         ACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT
genomic: GGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGT

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: 69 (upstream exon), 65 (downstream exon)
Score: 64

CAAGGATGACTTTTTTGATTCCCTCACTAGTGGAACATTTGGACGTGGAGGGCAAAACGGGAGGTCAAGATTTTCCGAACAGCGCAAACTAGATACAGAGgtacaaggtc ... ttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGTGGTTACCGTGGCGGCGGTCGCGCCCGTGGGTCATACTACGGTGGCAGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgctttcttgatgttgtaccatcactgttttgctgattgttgttttgtgcagACTTTTGGTGATTTCCCAAGGCATCGCCAGCCCTATCGTGGTGGGGGGCGTGGTTACCGTGGCGGCGGTCGCGCCCGTGGGTCATACTACGGTGGCAGAG
                                 tgctgat  putative branch site (score: 64)
                                          ttgtttt  putative PPT
                                          ttgtttt  TA-rich tract