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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgcacacccacacaaaccgcaaacgattctctccccctccccgtctctgtctctcagtttctttcttggatcggatggatctgctgcttcgccc...

Basic information

species Oryza sativa
transcript LOC_Os07g19060.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g19060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 2
TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccac---gcacacccacacaaaccgcaaacgattctctccccctccccgtctctgtctctcagtttctttcttggatcggatggatctgctgcttcgccc
|||| | ||||||||| ||| ||||| ||||||| || ||||| || ||||| ||||||||||||||||||||||| ||||| ||||||||| | ||||||||| ||     |||           | |      |||  | |    | | |  ||    ||  |   |    |   |||| | |    ||  ||     |  
TGGCAGTCTACTGCGGTGGCCTCTACACCGCCAAACCAGAGCTTGCTGCCCGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAGgtacaaccagaaacaattttttttctcccgttatgttcaattctttactcaggttccaagtccaaaccttaaccaatgatctg-tcatcctagtgtggttc--

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G123807_T02 (Zea mays), 5'ss of exon 2
TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgcacacccacacaaac-cgcaaacgattctctccccctccccgtctctgtctctcagtttctttcttggatcg-gatggatctgctgcttcgccc
|||| | ||||||||| ||| |||| ||||||||||| ||||| || ||||| ||||| |||||||||||||| ||||| || ||||||||| | ||||||||   |    | | |        | |      |  ||| |  || ||    ||||       ||| ||       | |   |  |||   |||  || |||
TGGCTGTCTACTGCGGTGGCCTCTATGCCGCCAAGCCAGAGCTTGCTGCCCGCCGCATTGAGGCCATCGGCTTTCAGGTTGGGCACCAGCTCTCTGAGAGgtatagccagaaacaattttttttctcctgttctgttcttcatctgcctaattctgcactcaggttcctagtccaaaccttaaccgatgatctg--tcaccc

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 5'ss of exon 1
TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgcacaccca--cacaaaccgcaaacgattctctccccctccccgtctct-gtctctcagtttctttcttggatcggatggatctgctgcttcgccc
|||||   ||| | ||| | ||||| ||   ||||||||| |||||||| ||  | ||||||||||| || |  |||||||||||||||||| |||||||||       ||||     ||    |  |   ||||    |    |      ||||| |  |   ||| |   |  | |||| || |    ||  |  |     
TGGCGATGTACAGTGGCCGATTCTATGCTAACAAGCCGGAACTCGCCGCTCGGAGGATCGAGGCCATTGGTTATCAGGTCGGCCACCAGCTCTCCGAGAGgtttgttttacacttgatcatcgtcttctttcgatctggttgatcattgtatctctaggttgctagtattagttgtagatctgaagatgatggcgaatgt---

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 1
TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacg---cacacccacacaaaccgcaaacgattctctccccctccccgtctctgtctctcagtttctttcttggatcggatggatctgctgcttcgccc
|| |  | || |||  | | |||||||||| ||||||||| |||||||||||| | ||||| ||||| |||| ||||||||||||||||||| ||||  ||||    |   | | | |   |   |   ||||  |   |   | |   | || ||  ||| |   | || ||  ||  |    |  |  ||  | ||  |  
TGTCCTCGTATTGCACCCGTTTCTACGCCGACAAGCCGGATCTCGCCGCCCGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtctctctctctttctctctctaaaccctataccttcaccttctgtttcattcttttcttatcatttctgattt---tctacttgtgggttttcaa

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ20859 (Selaginella moellendorffii), 5'ss of exon 1
TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgcacacccacacaaaccgcaaacgattctctccccctccccgtctctgtctctcagtttctttcttggatcggatggatctgctgcttcgccc-----------------------------------------------------------------------
||||| | ||||||| | |  |  |  |  |||||||||| || ||||| || || |||||||| |||||||||||||| || || |||||| | ||||||||  |    |   | || |  |     | || | |  |    ||  | |   |   |  ||||   | |  | | | |  || || | |   || |                                                                          
TGGCGACTTACTGCGACAGGCTACATTCTTCCAAGCCGGATCTGGCCGCTCGCCGGATCGAGGCGATCGGCTTCCAGGTGGGACAGCAGCTCGCGGAGAGgtaaaattttc-tgctcaaatgcttgcgaggaatgtggcttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggtggttttttcttctatcttttttcctctttccag

upper sequence: LOC_Os07g19060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ32385 (Selaginella moellendorffii), 5'ss of exon 1
TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtacca----cgcacacccacacaaaccgcaaacgattctctccccctccccgtctctgtctctcagtttctttc--ttggatcggatggatctgctgcttcgccc-----------------------------------------------------------------------------------------
||||| | ||||||| | |  |  |  |  |||||||||| || ||||| || || |||||||| |||||||||||||| || || |||||| | ||||||||  |    |  |||    |    | | |||| | ||              |  |   |  ||   | |  ||   |||| ||   ||||||||||   | ||                                                                                           
TGGCGACTTACTGCGACAGGCTACATTCTTCCAAGCCGGATCTGGCCGCTCGCCGGATCGAGGCGATCGGCTTCCAGGTGGGACAGCAGCTCGCGGAGAGgtaaaattttcttacattgccgtggagctcaaatgcttgcgaggaatgtg--gcttgcattccttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggtggttttttcttcgatcttttttcctctttccag

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|88422163|gb|CI688963.1|CI688963
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88581377|gb|CI698357.1|CI698357
EST:     GTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCCAC-AGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: GTCGCATCGAGGCCATCGGCTTCCAGGTCGGCC-ACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88329569|gb|CI650023.1|CI650023
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGCTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88578514|gb|CI687450.1|CI687450
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88388611|gb|CI683394.1|CI683394
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88572188|gb|CI663759.1|CI663759
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88296136|gb|CI667526.1|CI667526
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|86887581|gb|CI294215.1|CI294215
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
EST: gi|88573657|gb|CI665426.1|CI665426
EST:     CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAG                         ATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT
genomic: CGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATT

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: 72 (upstream exon), 70 (downstream exon)
Score: 30

TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgca ... tcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCGGCCTACTGCGGCGGCTTCTACGCCGCCAAGCCGGAGCTCGCCGCCCGTCGCATCGAGGCCATCGGCTTCCAGGTCGGCCACCAGCTCACCGAGAGgtaccacgcacacccacacaaaccgcaaacgattctctccccctccccgtctctgtctctcagtttctttcttggatcggatggatctgctgcttcgccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA