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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT

Basic information

species Oryza sativa
transcript LOC_Os01g68770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G058930_T01 (Zea mays), 3'ss of exon 6
cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
 |||    |   |  | |  |  || | ||| |||| ||   |  ||    ||  |    | | | |    |   |    ||    ||  || |  ||||||||||||||||||||||||| ||||||||||| ||||| |  ||||| || |||||  | ||||| ||||||||||||||||||||||| |||||||| 
aatagctgcatatgtatggcaaattgcttgacatgtgaagacagattcactatgctgatctcagtatcttgattaattattaagcctttgctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCTATAAGACTATGATCAGTTCATCATGGGGAGCCCCTGCAGCG

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G837351_T01 (Zea mays), 3'ss of exon 3
-cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
 |   ||    ||  ||   |   |  ||||  |   ||       | ||  ||  |    | | | |    |   |    ||    ||  || |    ||||||||||||||||||||||| ||||||||||| ||||| |  ||||| || ||||  |||||||| ||||||||||||||||||||||| |||||||| 
gctgcatatgtatggcaaattgcttgacatgtgaaaacagacagattcac-tatgctgatctcagtatcttgattaattattaagcctttgctacatttagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCACCACAAGACTATGATCAGTTCATCATGGGGAGCCCCTGCAGCG

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 3
cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataacca-----tagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
     |||  ||    ||  |  || | ||| |||| ||     |  | |   |||   ||||  |  |     | |  |     ||   ||   || |  ||||||||||||||||||||||||| ||||||||||| ||||| |  ||||| || ||||| |||||||| ||||||||||| ||||||||||| |||||||| 
-----tgcagatgtatggtaaaattgcttgacatgtgaaaaacagacagattcattatgatgatctcagtgtctttattacttattaagtttctgctacatgcagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
--------cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacac----atattt-gcatgactt---ttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
         |  |   |   |      ||| |   ||  |     ||   |    | |     |||| | || |   ||   ||||   | | | ||  ||| |  ||| |   || ||||| |||   ||  |||| || |||| ||| |||||||  ||||| |||||||| || ||||| ||||||||| | ||||||||||| || || || 
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatt-tatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 3
cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
                     | || ||  | |   || ||| ||||  |  |  |||  |  || ||        | ||| || |     || |  ||| ||||| || ||||| || || || |||| ||| ||||||| |||||| |||||||| |||||||| ||||||||  |||| ||||||||||||  ||| 
---------------gtatcttattgcaaaacaaagcattttctgttttagtttcttg--tcgctattagtcatatatcattgt-tggttattgtatcagGTGGGAGAAACCAGGACATAGTCCTTTGTATGGGTATGATTTTTGGTACCAACCTCGGCACAAGACCATGATCAGCACATCTTGGGGAGCACCTAAAGCC

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 3
cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataa----ccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
 |  ||| |||     | ||   ||   |  ||  | |    |  |   |||| |  |||     ||| ||   | |    |||     |||    | |  ||| ||||| || ||||| || || || |  |||||||| ||||  ||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||
gaacatgtccag---ggaatggttttagtataacatgagccaacctctgacat-tgagcacagtattttaagtttgattttccactccttttgatatatatcagATGGGAGAAACCAGGGCATAGTCCGTCTTTTGGCTACGATTTCTGGTACCAACCCCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ11187 (Selaginella moellendorffii), 3'ss of exon 3
cataatgcccattccaggatatgttc-catgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
                   || |||| | |||  | |    ||   | || |   |||   | ||| ||||        | | | || |  |  ||   || |||||||| | ||| ||||| ||||  |||||||| || | ||||||||||||||||||||| || |||||||||   || ||||| || ||  | || 
------------------gtaagttctcgtgagttcttgtctt---tcacgccattttttgtcactgttgag-------ctttggatcttacgact--tagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ15679 (Selaginella moellendorffii), 3'ss of exon 3
cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
      |    |||  |    | |  | |||  | |     |   | || |   |||   | ||||||||        | | | || |     ||   || |||||||| | ||| ||||| ||||  |||||||| || | ||||||||||||||||||||| || |||||||||   || ||||| || ||  | || 
------gtaagttctcgtgagt-tctcgtgagttcttgtcgt---tcacgccattttttgtcacttttgag-------ctttggatcttatgact--tagATGGGAAAAACAAGGACACAGTCCCTCTTTTGGCTACGACTTTTGGTATCAACCTCGTCACAAAACGATGATCAGTAGTTCCTGGGGGGCGCCCTCTGCG

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|11442705|gb|BF430608.1|BF430608
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|58658655|gb|CK047335.1|CK047335
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|33799340|gb|CF325529.1|CF325529
EST:     GGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|218504274|gb|FG947023.1|FG947023
EST:     GCTGGC-ATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|58654482|gb|CK043162.1|CK043162
EST:     TCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCGCAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: TCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|58669621|gb|CK058307.1|CK058307
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|29641234|gb|CB646241.1|CB646241
EST:     CTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGCGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATC
genomic: CTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAG-GACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATC
EST: gi|25797060|gb|CA753021.1|CA753021
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|29642049|gb|CB647056.1|CB647056
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|58594459|gb|CF992767.1|CF992767
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|33677794|gb|CF306033.1|CF306033
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|29660708|gb|CB656983.1|CB656983
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA
EST: gi|14571328|gb|BI118696.1|BI118696
EST:     GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTGAATGTCAAAGGACG                         TTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATKATTATTGGTATCA
genomic: GCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCA

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: 48

CATCTGGGGAGATAATGATTTCTTGCCTTGGGGATAAGGAGGGAAATGCTGCTGGCAATGGCTTCCTCCTGCTGGATTCTGAATTCAATGTCAAAGGACGgtgagttcct ... cttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT
                          agataac  putative branch site (score: 48)
                                      tatttcccttctcgc  putative PPT
                                  atagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacacatatttgcatgacttttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- -aatgccc
- - - - - - - - - - - -ttccatg
- - - - - - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - -acacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccata