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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGGAGACCTGGGATGAGGATGAGACGCATGATCCAGAAGTTCCTGCTGTTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgacctatgatctatactactgttaggtgtaatgctatgttttcatttgcgccccgcgcttttcttttgttttctatattggaaaattatttcatacctagatagcctagtagaaagaactgactaattaatggctttgactaaaatgttcag

Basic information

species Oryza sativa
transcript LOC_Os04g35190.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g35190.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G117633_T03 (Zea mays), 5'ss of exon 10
TGTGGAGACCTGGGATGAGGATGAGACGCATGATCCAGAAGTTCCTGCTGTTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgacctatgatctatactactgttaggtgtaatgctatgttttcatttgcgcccc-gcgcttttcttttgttttctatattggaaaattatttcatacctagatagcctagtagaaagaactgactaattaatggctttgactaaaatgttcag
 || |||  |||||| ||||||||||||||||| || || || ||||| ||| ||||||||||||||||| | || |||||||||||||| ||||||||||||               | || | ||  || || | |  |||   ||   | |     | | |  |    ||     | || |  |||    ||| || || ||    | |||||        ||| |||||||      ||| |||| | |||||
CGTTGAGGGCTGGGAGGAGGATGAGACGCATGACCCGGATGTGCCTGCCGTTTCCCACAGCAGGGGTTTGTCACCCTTTGTGTTTGTTCCGTTTGAGGAGgtac--------------attattttt--gtctagttcgctgtggccaaccgtgttggagggatggttaactgcaacttgtagttcaaat---ttttatgccgag----cgtagta--------tgattaattaactaaagtgagtaaattattcag

upper sequence: LOC_Os04g35190.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G155150_T01 (Zea mays), 5'ss of exon 6
TGTGGAGACCTGGGATGAGGATGAGACGCATGATCCAGAAGTTCCTGCTGTTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgacctatgatctatactactgttaggtgtaatgctatgttttcatttgcgccccgcgcttttcttttgttttctatattggaaaattatttcatacctagatagcctagtagaaagaactgactaattaatggctttgactaaaatgttcag
 || |||  |||||| ||||||||||||||||| ||||| |  ||||| ||| ||||||||||||| ||| | || | |||||||||||| ||||||||||||     |||  | |||| |  |||| |  || |           | || | |||    | ||  ||     ||       || ||  || ||| |  ||    | || |||||        ||| | |||||  |   |    ||| |||||||
CGTTGAGGGCTGGGAGGAGGATGAGACGCATGACCCAGACGCGCCTGCCGTTTCCCACAGCAGGGGCTTGTCACCCTCTGTGTTTGTTCCGTTTGAGGAGgtaca--ttatt-tttata-tcttgttcgcagtgac------cagccgttggagcc--atggttaactgcaacttg------tgcaattttgttttagtccc--ctggcatagtactgta---tgattgattaactgaagtacggaaattgttcag

upper sequence: LOC_Os04g35190.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S96_233V6.1 (Physcomitrella patens), 5'ss of exon 9
TGTGGAGACCTGGGATGAGGATGAGACGCATGATCCAGAAGTTCCTGCTGTTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgacctatgatctatactactgttaggtgtaatgctatgttttcatttgcgccccgcgcttttcttttgttttctatattggaaaattatttcatacctagatagcctagtagaaagaactgactaattaatggctttgactaaaatgttcag
 || ||    ||| | ||| ||||||| ||| |||||||  | || || ||| | ||| |  | ||  ||   ||||||||||||||||||||||| ||||||    ||||  |  || ||  |  ||   || | |   |   || ||  | | |||      ||||| ||| |   |     |  || | |   ||  | | |      ||   ||                                      
AGTTGACGGGTGGCAAGAGAATGAGACTCATAATCCAGACATACCAGCAGTTTCTCACCGGCGTGGCATGCAACCATTTGTGTTTGTTCCATTTGAAGAGgtaa---ctat--ttcatgctcttactaatggttacgtgctaaatttat--gggtccc------ttcttatgtatgagac----gggaactgtg--atgtcgaaaattttgagcgaaat-------------------------------------

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|86478979|gb|CI121612.1|CI121612
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|25806565|gb|CA762526.1|CA762526
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTAGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86834961|gb|CI346045.1|CI346045
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86889873|gb|CI333524.1|CI333524
EST:     GGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: GGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86832622|gb|CI345056.1|CI345056
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86878242|gb|CI319545.1|CI319545
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|89181378|gb|CI112884.1|CI112884
EST:     ACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAAATGGACTACTTTGTC
genomic: ACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86425348|gb|CI070445.1|CI070445
EST:     CCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: CCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86498168|gb|CI140801.1|CI140801
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|29645691|gb|CB650698.1|CB650698
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86505019|gb|CI147652.1|CI147652
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86486560|gb|CI129193.1|CI129193
EST:     TGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|29655902|gb|CB652177.1|CB652177
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGAAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|88228837|gb|CI226688.1|CI226688
EST:     TGACCCACATCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|29623230|gb|CB628241.1|CB628241
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|38471886|gb|CF956017.1|CF956017
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86481675|gb|CI124308.1|CI124308
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
EST: gi|86866146|gb|CI336846.1|CI336846
EST:     TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAG                         GCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC
genomic: TTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTC

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), 66 (downstream exon)
Score: 27

TGTGGAGACCTGGGATGAGGATGAGACGCATGATCCAGAAGTTCCTGCTGTTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgaccta ... aaatgttcagGCTGATACTTCAGTGATGAATCTGCCAGTGGAGAAGATGGACTACTTTGTCCCTGGGTGATCTTGCGCACAAATAATAGTTTTTCCAAGATATATGATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGGAGACCTGGGATGAGGATGAGACGCATGATCCAGAAGTTCCTGCTGTTACCCACAGCAGGGGTTTGACCCCATTTGTGTTTGTTCCATTTGAGGAGgtatgacctatgatctatactactgttaggtgtaatgctatgttttcatttgcgccccgcgcttttcttttgttttctatattggaaaattatttcatacctagatagcctagtagaaagaactgactaattaatggctttgactaaaatgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG