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

...ctctacgagcgtgtcgcgtgctgtattgcgtctgttttttttcatgttcagatgttgttcatgtttggatgttgatgcgagggtttttgcttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCCGGCCAAGGCCTTCAAATCACGCAAGGTTTATTACACTAACGAG

Basic information

species Oryza sativa
transcript LOC_Os09g32220.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 1
--------ctctacgagcgtgtcgcgtgctgtattgcgtctgttttttttcatgttcagatgttgttcatgtttggatgttgatgcgagggtt-tttgcttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCCGGCCAAGGCCTTCAAATCACGCAAGGTTTATTACACTAACGAG
         ||| ||||  | | |   || ||   | || |    || ||   | |||| |||||      |||    | |||   || | || |||||   |   |||||| ||||| || ||||||||||||||||||| |||  | |||| ||||||||||||||| |||||  ||||||||||||||||||| ||||||
aaatttgcatctgcgagtttattggaggccgt---gagtttaagcttctt-gcgctcagctgttg-----atttactagctgacatgatgtttctttgccgatctgcagGCAGGTGGTCATCAGGGCGAGGAACCTGAGGACCAACGCACAGTTCATCCCGGCCAAGGCTTTCAAGGCACGCAAGGTTTATTACACCAACGAG
















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|58589464|gb|CF987772.1|CF987772
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|66924228|gb|CX111076.1|CX111076
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|58686514|gb|CK075201.1|CK075201
EST:     CGCTCCCCGTCGGCGTCGNCCTCCCCCGAACCCAAGCTCGTCAAAGAGGG                         GCAAGTGGTAATTATGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|33682332|gb|CF310571.1|CF310571
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|88315160|gb|CI611824.1|CI611824
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|88393896|gb|CI684160.1|CI684160
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|88370009|gb|CI680691.1|CI680691
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|88578130|gb|CI674766.1|CI674766
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|33688252|gb|CF316491.1|CF316491
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|117242276|gb|CT842928.1|CT842928
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
EST: gi|33663183|gb|CF294150.1|CF294150
EST:     CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGG                         GCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC
genomic: CGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCC

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), 75 (downstream exon)
Score: 30

TGGTGATGGTGCTCATCGGCGTGCTCCGCTACTTCGTCGCCAAGCTGATGCGCTCCCCGTCGGCGTCGCCCTCCCCCGACCCCAAGCTCGTCAAGGAGGGgttcgttgct ... ttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCCGGCCAAGGCCTTCAAATCACGCAAGGTTTATTACACTAACGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagatgttgttcatgtttggatgttgatgcgagggtttttgcttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCCGGCCAAGGCCTTCAAATCACGCAAGGTTTATTACACTAACGAG
                        tgttgat  putative branch site (score: 30)
                                      tttttgctt  putative PPT
                                      ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctacgagcgtgtcgcgtgctgtattgcgtctgttttttttcatgttcagatgttgttcatgtttggatgttgatgcgagggtttttgcttgttcacagGCAAGTGGTAATTAGGGCGAGGAACCTGAGGATCAATTCGCAGTACATCCCGGCCAAGGCCTTCAAATCACGCAAGGTTTATTACACTAACGAG

- - - - - - - - cgtgctg
- - - - - - - - - - - - - -gcgtctg
- - - - - - - - - - - - - - - - - - - -tttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatg