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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGATCCTCCTGATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaaagctccctgtatgattcagcaatttcctttctagttgtgataaacacacaatatagttttcagaaactatataaaaaagaatgcaaataa...

Basic information

species Oryza sativa
transcript LOC_Os02g57400.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57400.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G123544_T01 (Zea mays), 5'ss of exon 6
GGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGATCCTCCTGATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaaagctccctgtatgattcagcaatttccttt---ctagttgtgataaacacac--aatatagttttcagaaactatataa----aaaagaatgcaaataa
||   ||      |     |     || || || ||||| || |||  |||||||| |||||| ||||| ||| | |||||||||||||| |||||||||||||   |  | ||  ||  |   |||  |||  |  |||    | ||| || |   |      |    ||       |   | |        |   | || |    | 
GGTCTATGTCAGCGAAGAAGAGGAAGAGGAGGAAGCTGACGACCCTTGTGATGCTGAAACTGATGAAGATCTATCCGATGAAGAAAGAGACATGCACGAGgtac-ggacgatctatctcaaatgttcgacaacctggtttggttttgttttgctttccttgtctagagaaggcactgaatgttcttccgcgtcacggggatacttgcag

upper sequence: LOC_Os02g57400.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G342327_T01 (Zea mays), 5'ss of exon 6
GGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGATCCTCCTGATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaaagctccctgtatgattcagcaatttcctttctagttgtgataaacacacaatat-agttttcagaaactatataaaaaagaatgcaaataa--------------------------
||| || || ||||| | ||| || || ||||| ||||| || |||| |||||||| |||||| || ||||||||||||||||||||||| ||||||||||||    |  |  |  ||   || | |  || |||     ||  || |  ||    ||| | || | |   | | || | |  | | ||   || |  |                            
GGAGGACTACTCAGTCTATGGCAGTGACGAAGAAGCTGACGACCCTCGTGATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtat-ggacgatttatctcagtg-tccgacattttttccccttattatc-tagtttcaccacatcaatacactgcaaatttgaagacaatgctgaatgttctctcgcgcatcaccggatgcttgcag
















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|218488536|gb|FG960950.1|FG960950
EST:     TGCTGGAACTGACGAAGACCCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: TGCTGGAACTGACGAAGA-CCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|86429440|gb|CI076121.1|CI076121
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|86855826|gb|CI271045.1|CI271045
EST:     ATGGTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|218482213|gb|FG969064.1|FG969064
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGCGGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|87031732|gb|CI272433.1|CI272433
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|29623882|gb|CB628893.1|CB628893
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|86536832|gb|CI177038.1|CI177038
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|29642503|gb|CB647510.1|CB647510
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|86477326|gb|CI119959.1|CI119959
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|5055992|gb|AU075371.1|AU075371
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|29642372|gb|CB647379.1|CB647379
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|218485764|gb|FG955746.1|FG955746
EST:     ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: ATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|88220906|gb|CI218757.1|CI218757
EST:     CTGATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
genomic: CTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATAC
EST: gi|33690966|gb|CF319205.1|CF319205
EST:     ATGAAGAAAGAGATATGCACGAG                         ATAGAAGCAGGCTCTGTTGATGAACACTCCCACCAAGTCCGACGAGGAATA
genomic: ATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACT-CCACCAAGTCCGACGAGGAATA

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: 70 (upstream exon), 72 (downstream exon)
Score: 14

GGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGATCCTCCTGATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaa ... attcctgcagATAGAAGCAGGCTCTGTTGATGAACACTCCACCAAGTCCGACGAGGAATACGACGATCTGGCAATGCAGGATGTGATGGAGAACGGTTACTGGTCCGACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGATCCTCCTGATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaaagctccctgtatgattcagcaatttcctttctagttgtgataaacacacaatatagttttcagaaactatataaaaaagaatgcaaataa

- - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaaa