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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGAGAGGGAAGATGAGTGCGGCATTTGCTTGGAGACTTGCACCAAGATGGTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgctccctctcacccttgcttatccgtttgagtatttaagtagtatatatatgatacccgtgcaacgatatttatcaattataggccccatgtc...

Basic information

species Oryza sativa
transcript LOC_Os01g67850.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67850.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G058450_T01 (Zea mays), 5'ss of exon 4
ACGAGAGGGAAGATGAGTGCGGCATTTGCTTGGAGACTTGCACCAAGATGGTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgctccctctcacccttgcttatccgtttgag--------tatttaagtagtatatatatgatacccgtgcaacgatatttatcaattataggccccatgtc
| || ||||| |||||||| ||||||||| ||||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||||||  ||||||||| || | |||||||||||||||| |        |||||||| |  | ||||||  |  | | ||   |||  |||||| |||  | ||| |    
ATGACAGGGAGGATGAGTGTGGCATTTGCCTGGAGACCTGCACCAAGATGGTCCTTCCGAATTGCAACCATGCCATGTGCATCAACTGTTACCGAGACTGgta--ttgctccctgtcgctcttgcttatccgtttggggggtgtattatttaagcaaca-atatatc-tgactgagcctggatcgttatcagttagggccccga----

upper sequence: LOC_Os01g67850.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA05G02960.1 (Glycine max), 5'ss of exon 5
ACGAGAGGGAAGATGAGTGCGGCATTTGCTTGGAGACTTGCACCAAGATGGTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatt-tgctccctctcacccttgcttatccgtttgagtatttaagtagtatatatatgatacccgtgcaacgatatttatca-attataggccccatgtc-----------------
  ||||| ||| ||||||| ||||||||||| ||| |||||||||| |||||  |||| ||||||  ||| |||||||| || || |||||  | ||| ||||||  |   | |  |  |||||   |   | | | | | ||    ||  |      | || |      |   |||||||  | ||  |        | |                  
TGGAGAGAGAACATGAGTGTGGCATTTGCTTAGAGTCTTGCACCAAAATGGTTTTTCCTAATTGCTGCCACGCCATGTGTATAAATTGTTACAGTGACGGgtaatcataagctcaatttcccttaaattaacttgtaattgttgttataagaatggagttattcttagcaattaatatttaatacatcttttattttttttaatctctttatgatacag

upper sequence: LOC_Os01g67850.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0010g02200.t01 (Vitis vinifera), 5'ss of exon 4
ACGAGAGGGAAGATGAGTGCGGCATTTGCTTGGAGACTTGCACCAAGATGGTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgctccctctcacccttgcttatccgtt---------tgagtatttaagtagtatatatatgatacccgtgcaacgatatttatcaattataggccccatgtc-----------------
   | ||||||||||| || || ||||| |||||| |||||||||| |||||| | || ||||||   ||||| |||||||||||||| || || ||||||||| ||| |  ||   |   |||  | | | ||           |  | ||    | |  ||| |||| |  | |  |  | ||||| ||  ||| |  |  | | |                  
TGAAAAGGGAAGATGAATGTGGAATTTGTTTGGAGCCTTGCACCAAAATGGTCTTGCCTAATTGCTGTCATGCAATGTGCATCAACTGCTACCGTGACTGgtaagttggtaactacaaggattgtattttctttattctgtctctaacactttccaactgcatacatgagattc-tagactgctatttttct-ttacactcttcctcttctttatccaaattacag

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|41883723|gb|BX928570.1|BX928570
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|33693004|gb|CF321243.1|CF321243
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCT
EST: gi|33685056|gb|CF313295.1|CF313295
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|3766680|gb|AU030790.1|AU030790
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTNTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|33693005|gb|CF321244.1|CF321244
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|88985618|gb|CI016327.1|CI016327
EST:     TGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: TGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|33693590|gb|CF321829.1|CF321829
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|88956854|gb|CI009076.1|CI009076
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|9884501|gb|BE607334.1|BE607334
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|86834866|gb|CI345950.1|CI345950
EST:     CTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: CTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|88983314|gb|CI028551.1|CI028551
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|86415656|gb|CI029667.1|CI029667
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|33688530|gb|CF316769.1|CF316769
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|88543210|gb|CI473200.1|CI473200
EST:     GTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|33691280|gb|CF319519.1|CF319519
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|33680393|gb|CF308632.1|CF308632
EST:     CATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: CATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|87030695|gb|CI361909.1|CI361909
EST:     TATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: TATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|66920252|gb|CX107100.1|CX107100
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|15850824|gb|BI799100.1|BI799100
EST:     GTCCTTCC-AA-TGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|88835319|gb|CI005009.1|CI005009
EST:     CATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: CATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|89191395|gb|CI393248.1|CI393248
EST:     CTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: CTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
EST: gi|33679207|gb|CF307446.1|CF307446
EST:     GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTG                         GTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT
genomic: GTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGT

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: 75 (upstream exon), 73 (downstream exon)
Score: 35

ACGAGAGGGAAGATGAGTGCGGCATTTGCTTGGAGACTTGCACCAAGATGGTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgct ... gggttttcagGTACACAAGATCTCAGTCATGCCCGTTCTGCCGCGGGAGCCTGAAGAGAGTCCGATCAAGGGACCTCTGGGTGCTCACCGGAGACGACGACGTGATCGAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGAGAGGGAAGATGAGTGCGGCATTTGCTTGGAGACTTGCACCAAGATGGTCCTTCCAAATTGCAACCATGCCATGTGCATCAACTGTTATCGAGACTGgtaatttgctccctctcacccttgcttatccgtttgagtatttaagtagtatatatatgatacccgtgcaacgatatttatcaattataggccccatgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctc