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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagatgtggtctttcacatattgacagcttttgtacaaacaagttatttacggaaatgactgaggcggctttgcttatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAGGTGTTGTAGGTACAGGAGGTGCTGATGGCACTGCTTATATAT

Basic information

species Oryza sativa
transcript LOC_Os08g02330.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G132286_T01 (Zea mays), 3'ss of exon 9
gtaaagatgtggtctttcacatattgacagcttttgtacaaacaagttatttacggaaatgactgaggcggctt---------------tgcttatattt-cagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAG--GTGTTGTAGGTACAGGAGGTGCTGATGGCACTGCTTATATAT
||||| |    | |  | |   |    ||   | |      |  |||       | | || || ||| |||| |               || || ||||| ||||| ||||||||| ||||||||||||||||||||||| |||||| ||||||||||||||  ||||  |||                                 
gtaaaaactctgaccattaggcacactcactctgtagtggtattagtggacagtgtatataacagagccggcctactgctgcatctcgctgtttttattttcagGGCGAGCCCCTCGAAGACTCCCGTGCGTCCCCGTGCGCCTCGCTAGCTGATGCACTAGAGGTGTCCTAG---------------------------------

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G069102_T03 (Zea mays), 3'ss of exon 8
gtaaagatgtggtctttcacatattgacagcttttgtacaaacaagttattta--cgg--aaatgactgaggcggctttgcttatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAGGTGTTGTAGGTACAGGAGGTGCTGATGG---CACTGCTTATATAT
|||||  | ||     ||   |   |       |||   ||  |  |  | |   |||    |  || ||| ||   | |  | | ||||||||||||||| || ||||| |||||||||||||| |  |||||||| ||||||   ||   | | ||  |||| |||||||||| |    ||||||| |||   
gtaaaactctgactgatcttcttacgctttgcattgagtaaggagctcttctgggcggttggacaacagagtcgttctcgtgtgt-tttcagGGTGAGCCCGTCCAAGACGCCCGTGCGTCCCCGCGTCCCTCGCCACCTGATGTCGTACTAGGTATACATACATGAGGTGCTGACGATGCCACTGCTCATA---

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G173428_T03 (Zea mays), 3'ss of exon 1
gtaaaga-tgtggtctttc-acatattgaca--gcttttgtacaa----acaagttattta-cggaaatg----actgaggcggctt--tgcttatattt-cagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAG--GTGTTGTAGGTACAGGAGGTGCTGATGGCACTGCTTATATAT
||||| | | ||  | ||  ||| | | ||   ||  | |||  |    |||   ||| || | ||   |    ||||  ||  ||   || || ||||| ||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||  ||||  |||||||||||||||| || ||||||||||||||  
gtaaaaactctgaccattagacacactcactctgcagtggtattactggacactgtatataacagaggcggcctactgctgcatctcgctgtttttattttcagGGTGAGCCCCTCGAAGACTCCCGTGCGTCCCCGTGCGCCTCGCCAGCTGATGCACTAGAGGTGTCCTAGGTACAGGAGGTGCGGAAGGCACTGCTTATAT--

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G349794_T01 (Zea mays), 3'ss of exon 10
gtaaagatgtggtctttcacatattgacagcttttgtacaaacaagttattt--acgg--aaatgactgaggcggctttgcttatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAGGTGTTGTAGGTACAGGAGGTGCTGA---TGGCACTGCTTATATAT
|||||  | ||     ||   |   |       |||   ||  |  |  | |  ||||    || || ||| ||   |    | | ||||||||||| ||| || ||||| |||||||||||||| |  |||||||||||||||   |    | | ||  |||||||||||||||   |||||||||| |||   
gtaaaactctgactgatcttcttacgctttgcattgaggaaggagctcttctggacggttggataacagagccgttctaatgtgt-tttcagGGTGAACCCGTCCAAGACGCCCGTGCGTCCCCGCGACCCTCGCCAGCTGATGTCATCCTAGGTATACATACAGGAGGTGCTGACAATGGCACTGCTCATA---

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G161649_T01 (Zea mays), 3'ss of exon 7
gtaaagatgtggtctttcacatattgacagcttttgtacaaaca--agttatttacggaaatgactgaggcggctt---------------tgcttatattt-cagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAG--GTGTTGTAGGTACAGGAGGTGCTGATGGCACTGCTTATATAT
||||| |    | |  | | | |   |||   | || |     |  |||       | | || || ||| |||| |               || || ||||| ||||||||||||||| |||||||||||||||||| |||| |||||||||||||||||||||  ||||  |||||||||||||||  || ||||||||||||||  
gtaaaaactctgaccattagacacacacacactctgcagtggtattagtggacactgtatataacagagccggcctactgctgcatctcgctgtttttattttcagGGTGAGCCCCTCGAAGACTCCCGTGCGTCCCTGTGCGCCTCGCCAGCTGATGCACTAGAGGTGTCCTAGGTACAGGAGGTGTGGAAGGCACTGCTTATAT--

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|86899176|gb|CI298078.1|CI298078
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCG
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCG
EST: gi|87029144|gb|CI276412.1|CI276412
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
EST: gi|86495223|gb|CI137856.1|CI137856
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
EST: gi|86849377|gb|CI297825.1|CI297825
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
EST: gi|29646834|gb|CB651841.1|CB651841
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
EST: gi|29643786|gb|CB648793.1|CB648793
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
EST: gi|29646833|gb|CB651840.1|CB651840
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
EST: gi|86859325|gb|CI278774.1|CI278774
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
EST: gi|218493611|gb|FG968673.1|FG968673
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
EST: gi|86495871|gb|CI138504.1|CI138504
EST:     ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAG                         GGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT
genomic: ACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGAT

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: 57 (upstream exon), 38 (downstream exon)
Score: 8

GCTGAAAGTGCCACTGCTGCTCTCAACTGCAGTGGTGTCATACTGGGTTCCTTGCCAATAAGgtaaagatgt ... tatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAGGTGTTGTAGGTACAGGAGGTGCTGATGGCACTGCTTATATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtacaaacaagttatttacggaaatgactgaggcggctttgcttatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAGGTGTTGTAGGTACAGGAGGTGCTGATGGCACTGCTTATATAT
                                      ctttgctt  CT-rich tract
      aaacaagttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagatgtggtctttcacatattgacagcttttgtacaaacaagttatttacggaaatgactgaggcggctttgcttatatttcagGGTGAGCCCCTCAAAGACTCCCGTGCGTCCCCGTGCACCTCGCCAGCTGATGCACTAGGTGTTGTAGGTACAGGAGGTGCTGATGGCACTGCTTATATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT