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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACCGAAGTCATTGCCCGGGGAATGGATTTCAAAGGTGTTAACTGCGTTATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatctggctttgacaggctacacgcacccgtctgtgcatttttgtgaatgatgtcttgtacataagcatctgcgtggaaggcctgagttctgatg...

Basic information

species Oryza sativa
transcript LOC_Os07g45360.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g45360.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G083580_T02 (Zea mays), 5'ss of exon 10
GCTACCGAAGTCATTGCCCGGGGAATGGATTTCAAAGGTGTTAACTGCGTTATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaag-----tatctggctttgacaggctacacgcacccgtctgtgcatttttgtgaatgatgtcttgtacataagcatctgcgtggaaggcctgagttctgatg
|| || ||||||||||||||||||||||| |||||||||||   ||  || || ||||| |||||||| ||||| ||| |||||||||||||| | |||||||||      || ||| |||||| | |    | |    | |||  || |        ||||| | ||  |       |     ||   ||| | | |  ||   
GCAACGGAAGTCATTGCCCGGGGAATGGACTTCAAAGGTGTCGCCTCTGTGATAAACTACGATTTTCCGGAGTCGGCTGCTGCCTATATTCACAGGATAGgtaagaaagacatttggatttgactgtcgtggcacttgtgcctgcacactcacaatgttgatg-cctgagctctgatgtacatttgattggc-tcaatgttg---

upper sequence: LOC_Os07g45360.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA03G33590.1 (Glycine max), 5'ss of exon 11
GCTACCGAAGTCATTGCCCGGGGAATGGATTTCAAAGGTGTTAACTGCGTTATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatc-tggctttgacag-gctacacgcacccgtctgtgcatttttgtgaatgatgtcttgtacataagcatctgcgtggaaggcctgagttctgatg----------------------------------------------------------
||||| || ||  |||||||||| ||||||||||||||||| ||||| || ||||| |||||||| || || || ||| |||| ||| | ||| |||| |||| ||    |    || |    | |  |     | |       |||| || | || ||   |||||  | |   ||| | ||||    ||   ||   |                                                            
GCTACTGATGTAGTTGCCCGGGGCATGGATTTCAAAGGTGTGAACTGTGTGATCAATTATGATTTCCCTGATTCTGCTGCTGCATATGTCCACAGAATTGgtacgtgcagttatattaatgttgttttagatttcagaaaagatatttatg-ggattataatttgta--ttattctct-catggagcctcttgattgctagattaatgaattattattactattattatttgctaatagaaaatgttgatttttcattag

upper sequence: LOC_Os07g45360.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA19G36300.2 (Glycine max), 5'ss of exon 11
GCTACCGAAGTCATTGCCCGGGGAATGGATTTCAAAGGTGTTAACTGCGTTATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatctggctttgacaggctacacgcacccgtctgtgcatttttgtgaatgatgtcttgtacataagcatctgcgtggaaggcctgagttctgatg----------------------------------------------------
||||| || ||  ||||||| || ||||||||||||||||| ||||| || ||||| |||||||| || || || ||| |||| ||| | ||| |||| |||| ||       | | |  |         |   |       || ||| |      | |  | || || |   ||| | ||||    ||   ||   |                                                      
GCTACTGATGTAGTTGCCCGTGGCATGGATTTCAAAGGTGTGAACTGTGTGATCAATTATGATTTCCCCGATTCTGCTGCTGCTTATGTCCACAGAATTGgtacgtgcagttatattaatgttgttttagatttgggaaaagatatttatagggattataatttatattattctct-catggagcctctcgattgctagatcactcaattattattattatttgctaatagaaaatgttgatttttcattag

upper sequence: LOC_Os07g45360.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G09720.1 (Arabidopsis thaliana), 5'ss of exon 12
GCTACCGAAGTCATTGCCCGGGGAATGGATTTCAAAGGTGTTAACTGCGTTATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatctggctttgacagg-----ctacacgca---cccgtctgtgcatttttgtgaatgatgtcttgtacataagcatctgcgtggaaggcctgagttctgatg--------
|| || || || |||||| | || ||||||||||||||  | |||||||| || ||||||||||| || || ||||||||||| || || ||| | || |||| | || |   | | ||  |      |  |   |   |   | |   |  || | |||  |   | ||  |   | |  |    ||    |||||   || | ||         
GCCACTGATGTGATTGCCAGAGGTATGGATTTCAAAGGCATCAACTGCGTGATAAACTATGATTTCCCGGATTCAGCTTCTGCATACATCCACAGGATTGgtacgcatattattattactagagcctttgtatctaaatcttatattctctgttctatgagagtcatttttgatg-atgagttgatgtatttggcctc--ttttaatacatttcag

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|88200073|gb|CI199923.1|CI199923
EST:     TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAG                         GACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
genomic: TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
EST: gi|29615362|gb|CB620374.1|CB620374
EST:     TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACAGAATAG                         GACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCCCCG
genomic: TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
EST: gi|89176536|gb|CI111575.1|CI111575
EST:     TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAG                         GACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
genomic: TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
EST: gi|218499846|gb|FG954109.1|FG954109
EST:     TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAG                         GACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCAAATTCTTCACCG
genomic: TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
EST: gi|88201323|gb|CI201678.1|CI201678
EST:     TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAG                         GACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
genomic: TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
EST: gi|89161943|gb|CI102291.1|CI102291
EST:     TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAG                         GACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
genomic: TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
EST: gi|89185206|gb|CI050940.1|CI050940
EST:     TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAG                         GACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
genomic: TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
EST: gi|29664206|gb|CB660481.1|CB660481
EST:     TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAG                         GACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG
genomic: TATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCG

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), 71 (downstream exon)
Score: 7

GCTACCGAAGTCATTGCCCGGGGAATGGATTTCAAAGGTGTTAACTGCGTTATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatct ... tgttatatagGACGATCTGGAAGAGCAGGTAGATCAGGGGAGGCCATCACATTCTTCACCGAGGAGGATAAGCCATTCTTGCGGAACATCGCAAATGTGCTGATATCTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACCGAAGTCATTGCCCGGGGAATGGATTTCAAAGGTGTTAACTGCGTTATCAACTATGATTTTCCAGAGTCAGCTTCTGCCTATATTCACCGAATAGgtaagtatctggctttgacaggctacacgcacccgtctgtgcatttttgtgaatgatgtcttgtacataagcatctgcgtggaaggcctgagttctgatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcaccc