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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttgtgattattttatgttgtcatatatgttgtattgcgtagcatctaagttttatggtgcccctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG

Basic information

species Oryza sativa
transcript LOC_Os03g49150.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G856436_T02 (Zea mays), 3'ss of exon 3
gtaagatttgtgattattttatgttgtcatatatgttgtattgcgtagcatctaagtttt-atggtgcccctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG
||||||||||  |   || | |  |    |   |  | |||||| | ||||||| ||||| ||| ||| | | |||||||| ||||| ||||||||||||||||| ||||||||||| || |||||| | |||||
gtaagatttgcaacggttatttcgtagtgttcttcgtatattgccttgcatctatgtttttatgatgctctt-ctctagGAGGCTGCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG

upper sequence: LOC_Os03g49150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G832740_T01 (Zea mays), 3'ss of exon 3
gtaagatttgtga---ttattttatgttgtcatatatgttgtattgcgtagcatctaagtttt-atggtgcccctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG
|||||||||| ||   || ||| ||  |||| |   |||  |||||| | ||| |||| |||| |||  || | | |||||||| || |||||||||||| ||||||| ||||||||||| || |||||| | |||||
gtaagatttgcgaaggttgtttcatagtgtc-tccttgt-atattgccttgcacctaactttttatgacgctctt-ctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG
















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|88844230|gb|CI005603.1|CI005603
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|88240560|gb|CI239722.1|CI239722
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|86825997|gb|CI362437.1|CI362437
EST:     ATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: ATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|9865632|gb|AU101382.1|AU101382
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|86884896|gb|CI314472.1|CI314472
EST:     GTCTGATATCTTCTGTGTTGGCTCCGGATCCACTTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: GTCTGATATCTTCTGTGTTGGCTGCGGATCCA-TTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|86832532|gb|CI344782.1|CI344782
EST:     ATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: ATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|86886993|gb|CI324414.1|CI324414
EST:     TGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|218479417|gb|FG947989.1|FG947989
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTATA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|33691799|gb|CF320038.1|CF320038
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|86419787|gb|CI054588.1|CI054588
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|8858378|gb|AU095696.1|AU095696
EST:     GTCTTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: GTC-TGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|58662158|gb|CK050838.1|CK050838
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGGAAGGGAAATTTATTTT
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAA-GGAAGGGAAATTTATTTT
EST: gi|88205477|gb|CI205326.1|CI205326
EST:     CGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|87013174|gb|CI281688.1|CI281688
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|87023464|gb|CI284611.1|CI284611
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|58663165|gb|CK051851.1|CK051851
EST:     TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: TGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|86417196|gb|CI031405.1|CI031405
EST:     GATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
genomic: GATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTA
EST: gi|88251691|gb|CI350119.1|CI350119
EST:     GTTGGCTGCGGATCCATTGTTGGATGGAAATAT                         GAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGGAAATTTATTTT
genomic: GTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAA-GGGAAATTTATTTT

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), 56 (downstream exon)
Score: 86

GACTTCTGGAGTAAAAGAGGATCGCATGATGATAACCGGAATGCATACTGTGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttg ... cctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcatatatgttgtattgcgtagcatctaagttttatggtgcccctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG
                                           cccctactct  CT-rich tract
     atatatgttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatttgtgattattttatgttgtcatatatgttgtattgcgtagcatctaagttttatggtgcccctactctagGAAGCTGCACATGAGAAGAGCCAGAGGTACAAGGAAGGGAAATTTATTTTAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA