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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGGAAGAGGTTTAGAGGGGAAGACAAACCCCCGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgtcactttcccccatcataatctatcttgcttctatatttagtattagcagctaacgtacgtggcagtgaggtaccatataggtggggaacc...

Basic information

species Oryza sativa
transcript LOC_Os05g23860.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G435373_T01 (Zea mays), 5'ss of exon 3
CTGTGGAAGAGGTTTAGAGGGGAAGACAAACCCCCGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgtcactttcccccatcataatctatcttgcttctatatttagtattagcagctaacgtacgtggcagt----gaggtaccatataggtggggaacc
|| |||||||||||||||||||||||||| ||||| || ||||| ||  |||||| ||| |||||||| || ||||| ||||||||||||| | |  |||  |  ||   ||  | |||| ||   |  ||||  |  | |||||||  |  |  | | |    | |  | |||| |  |   ||   
CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAGgtgcaacagcc--tttatcatatgcaaacatgtctttctagcacctttatcagca-cagctaatatttgcagaaatacctgtgagatcataaatataacgaca-

upper sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 3
CTGTGGAAGAGGTTTAGAGGGGAAGACAAACCCCCGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgtcactttcccccatcataatctatcttgcttctatatt--tagtattagcagct-aacgtacgtggcagt-gaggtaccatataggtggggaacc
|| |||||||||||||||||||||||||| ||||| || ||||| ||  |||||| ||| |||||||| || ||||| |||||||||||||   ||    ||   ||||||  | | | || || | ||       | | ||||| | | |  |  |   | | | || |  |  |  | |  ||   
CTCTGGAAGAGGTTTAGAGGGGAAGACAAGCCCCCAGCACATCTAGGTGCAAGCAGAGACTACAATGTGGACATGGTGCCAAAGgtgcaac-accaacggcctttatcatatgcaaacatgtttttctagcacctttgtcagcagttcagcacagataatatttgcggaaatacctgcgagatga---

upper sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 3
CTGTGGAAGAGGTTTAGAGGGGAAGACAAACCCCCGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgtcactttcccccatcataatctatcttgcttctatatttagtattagcagctaacgta-cgtggcagtgaggtaccatataggtggggaacc-
|| |||||||||||||| ||||||||||| || ||||| ||||| ||  |||||| ||||||||||||||| ||||| |||||||||  |   |  |     ||||    |   || || |||  | |  ||| | ||    || || |   | |   | |  |  |  |||| |      |||  
CTCTGGAAGAGGTTTAGGGGGGAAGACAAGCCACCGGCACATCTAGGTGCAAGCAGAGATTACAATGTAGACATGGTTCCAAAGgtgtgataatt-cccgatcccaatggaccgtacctagcta-tgtgcttattgtttcttgccaaggcctcatcatacttggcaaatatattgactaaaaacat

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|88765626|gb|CI774720.1|CI774720
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCT
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCT
EST: gi|2310891|gb|C27046.1|C27046
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACC
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACC
EST: gi|88399430|gb|CI606051.1|CI606051
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|88315062|gb|CI610121.1|CI610121
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|88400779|gb|CI616784.1|CI616784
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACAC
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACAC
EST: gi|58679926|gb|CK068613.1|CK068613
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|33655822|gb|CF278436.1|CF278436
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|88425765|gb|CI571665.1|CI571665
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|58600989|gb|CK011517.1|CK011517
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|88421949|gb|CI611569.1|CI611569
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|27577069|gb|CA999763.1|CA999763
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|88735490|gb|CI758998.1|CI758998
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|58607180|gb|CK035213.1|CK035213
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATCTGGTCCCAAAG                         TTTATGATGGCCAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTT
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGT-
EST: gi|88392817|gb|CI624048.1|CI624048
EST:     GGCTCATCTGGGCTCAAGCAAAGATTACAACTGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: GGCTCATCTGGGCTCAAGCAAAGATTACAA-TGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|58673621|gb|CK062307.1|CK062307
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|33655650|gb|CF278264.1|CF278264
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|88726752|gb|CI750407.1|CI750407
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|58668576|gb|CK057262.1|CK057262
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
EST: gi|58687035|gb|CK075722.1|CK075722
EST:     CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAG                         TTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG
genomic: CGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTG

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: 58 (upstream exon), 70 (downstream exon)
Score: 35

CTGTGGAAGAGGTTTAGAGGGGAAGACAAACCCCCGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgt ... atctcggcagTTTATGATGGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTGACAAAGTATTTGTCATTCAAAGCTGTCGATGGAAGCTATGTCTTCAGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTGGAAGAGGTTTAGAGGGGAAGACAAACCCCCGGCTCATCTGGGCTCAAGCAAAGATTACAATGTAGATATGGTCCCAAAGgtgcaactgtcactttcccccatcataatctatcttgcttctatatttagtattagcagctaacgtacgtggcagtgaggtaccatataggtggggaacc

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgggg