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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttggtaatacttttagagcttgctttgattttgttcattgctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA

Basic information

species Oryza sativa
transcript LOC_Os08g23440.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G432083_T01 (Zea mays), 3'ss of exon 3
aatgttggt--aatacttttagagcttgctttgattttgttcattgct-gcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
  | ||| |  ||| ||   | |   | ||||   ||  |  | || |   | | || ||  | || || |      |||  | ||| ||  |||| | |||||||||||||||||| ||||| || || ||||| ||||||||||||||||||||||| || ||| ||||||||||||| || |||||||| ||||||||||
--tcttgattcaatgctgggacaaagtactttttgttgttctagtgttcaaccaaaacaaactaac-gccaacaaactgacttgcatgttgaatgacctatagGGTGGTGGGCCATATTATCTTATAGGCCGTGCACTTGGTCCTGAAGTTGGAGTTAGTATAGGATTATGCTTCTTCCTCGGGAATGCAGTGGCTGGATCCA

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
---aatgttggtaatacttttagagcttgctttgattt-tgttcattgctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
      |||  | | |       |||      | |  |   || | |     |||| || |  |||     || |||| |   ||  || | |||| ||  |||||||| || || ||||||||||| || ||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||| ||| |  
aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgat----atagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
-----aatgttggtaatacttttagagcttgctttgattttgttcattgctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
     ||       |  | ||||    |        | | |  |   |    |  || || | ||||     || |||| |   ||  || | |||| ||  |||||||| || || ||||||||||| || ||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||| ||| |  
tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaatt-ctaacactcattaataattgat----atagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------------------------------------------------aatgttggtaatacttt-tagagcttgctttgattttgttcattgc-tgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
                                                                                                | | |   ||| ||   |   |||  |    || | ||  ||   ||  |  |     || |   |      |||  |  | | ||||       |  ||||||| || ||||| || |||||||| || || |||||||| ||||||||  ||||||| ||  ||||||| || ||||| ||||||||||||||| |  
gtaattcttttttctgttatatcacctaaattttctttgaataaaactatgtaaccataattaaagatattcctccctctcttgggtctctgcctctctggtccataattgacaccccttattacttttctatttcttttgtgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
aatgttggtaatacttttagagcttgctttgattttgttcatt--gctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
    ||  |||  ||| |    || |||| |  ||  ||| ||  | || |  |      || |  |  |    | |  | |       |  |  |   |||||||| |||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||  
--ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaattgataccaatctattttcttgacatctttgtttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------aatgttggtaatacttttagagcttgctttgattttgttcattgctgcctataaaaacttgaccgcgattgttttgatgt----------tcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
                                                                                          | ||  | | |      | ||| |||     | ||  || | ||||  ||   | |  | ||   ||| ||     |  |          | |  | || ||      ||||||| || ||||||||||| || || || || ||||||||||| ||||| || || || ||||| || |||||||| ||||| || ||||||||| | |
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaat-gagattgtaccaacttc-ttgactgctttctg-gacatttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S5_444V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------aatgttggtaatactttta----gagcttgctttgattttgttcatt-----gctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatcc----atagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
                                                   | || | |||||| ||      ||      |  || |   |||||      ||   |||   ||   |   |   |   |  |||    |  |||||| || |    | ||||||| || || || || || || || || || |||||||| || |||||||| || |||||| | || |||||||| || ||||||||||||| |||  
gttagtatcttgagtaaaggaatttcatgtgtcgaaattcaatcaatcatgtatttgcaatactcttgtctcaaggacatatgcatgtaaatcatttaaggactttatatttgaagcagtttgtcttccataagattccaacgttttatcattctattacagGGTGGGGGTCCCTATTACCTGATAGGTCGGGCTCTTGGTCCAGAGGTTGGAGTAAGTATTGGATTGTGTTTCTTCCTGGGCAATGCAGTTGCTGCATCAT

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ23975 (Selaginella moellendorffii), 3'ss of exon 3
aatgttggtaatacttttagagcttgctttgattttgttcattgctgcctataaaaacttg-accgcgattgttttgatgttcatttttta-tgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
                                                 |  ||||  |||    ||||  |||||  | ||  ||    | || |  ||||||||| || || || ||||| ||||| || || |||||||| ||||| ||  |||| ||||| || ||||| |||||||||||||| |||||||||||  
------------------------------------------------gttcaaaattttgcgttgcgacagtttttcttttggttaagcactggtttatagGGTGGCGGACCGTATTATCTGATTGGTCGAGCTCTTGGTCCGGAAGTCGGTATTAGTATTGGGCTTTGCTTTTTCCTTGGAAATGCGGTTGCTGGATCAC

upper sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ21598 (Selaginella moellendorffii), 3'ss of exon 3
aatgttggtaatacttttagagcttgctttgattttgttcattgctgcctataaaaacttg-accgcgattgttttgatgttcatttttta-tgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
                                                 |   |||  |||    ||||  |||||  | ||  ||    | || |  ||||||||| || || || ||||| ||||| || || |||||||| ||||| ||  |||| ||||| || ||||| |||||||||||||| |||||||||||  
------------------------------------------------gttcgaaattttgcgttgcgacagtttttcttttggttaagcactgctttatagGGTGGCGGACCGTATTATCTGATTGGTCGAGCTCTTGGTCCGGAAGTCGGTATTAGTATTGGGCTTTGCTTTTTCCTTGGAAATGCGGTTGCTGGATCAC

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|58693751|gb|CK082438.1|CK082438
EST:     TTTTAACTGGAATATCATTAAGTGCCATTGCAACGAATGCAGCAATGAAG                         GGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGA
genomic: TTTTAACTGGAATATCATTAAGTGCCATTGCAACGAATGGAGCAATGAAGgtacgctgaa ... tgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGA




















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: 71 (upstream exon), 62 (downstream exon)
Score: 14

AGGTGTATGGCAGTCGCTTGTTTTAGTCTCGTTCTGTGGTGCATGCACATTTTTAACTGGAATATCATTAAGTGCCATTGCAACGAATGGAGCAATGAAGgtacgctgaa ... tgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
                          ttttgat  putative branch site (score: 14)
                                      ttttttat  putative PPT
                               atgttcattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgttggtaatacttttagagcttgctttgattttgttcattgctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
aatgttg
- - - - - - - - - - agcttgc
- - - - - - - - - - - - - - - - - - - - - tgctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgatg