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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaatacatatccttatgtaatctgcagttttaaatgttgtagatattcccaacgcatgaactctgtacagcacataaattcctcttacgatggtacgttttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCCGATGCCGAGAAGGCATACTACTTATCACAAGGAATCACACCACCCAACT

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 13
gtaagcaaatacat-atccttatgtaatctgcagttttaaatgttgtagatattcccaacgcatgaactctgtacagcacataaattcctcttacgatggtacgttttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCCGATGCCGAGAAGGCATACTACTTATCACAAGGAATCACACCACCCAACT
       | ||||| ||  ||        ||||  ||| | ||||   |  |  | |   |  |  | | || |     | |||   |   |||   | | | || |   | ||||||||||||||||| || |||||||||| ||||||||| || |||||||| ||||| |||||||| || |||||    | ||| |||||||| || ||||
-------agtacattatatttcaaaggcatgca--tttgactgttac-ggcacccaccctgtgtcca-tatggattttgcttaa---ctgtttaaacttggatgtct-accacagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCGGAGAAGGCTTATTACTTGGAGCGAGGCATCACACCCCCGAACT

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G006507_T01 (Zea mays), 3'ss of exon 1
-----------------gtaagcaaatacatatccttatgtaatctgcagttttaaatg--ttgtagatattcccaacgcatgaactctgtacagcacataaattcctcttacgatggtacgttt---tgtct----cagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCCGATGCCGAGAAGGCATACTACTTATCACAAGGAATCACACCACCCAACT
                  || |  | |   | |  | |    || |    ||| |||||  |  |   || | | |  |||| |||| ||||   ||  |  |||    |||      |||  ||   ||||      |||||||||||||||| || |||||||||| ||||||||| || |||||||| ||||| |||||||| || |||||      ||| ||||| || || || |
gtaaggtggtacttgtactatgttatttggttttttcacagtatattatatttcaaatgcatgatttttactgctacggcatcaactatgtatc-catttggattttctttaattgtctacacttaattgtccaccatagGTAAGAGCACGCTGCAGAAAAGAATGGGGGATATTTCAGACAAGGCTGGCTGATGCAGAGAAGGCTTATTACTTGGAGAGAGGCATCACGCCCCCGAATT
















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|89168225|gb|CI109429.1|CI109429
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|29673249|gb|CB669524.1|CB669524
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|86851667|gb|CI315245.1|CI315245
EST:     GAATGGAAAAGCACCAT-GGAAGGG                         GTAAGAGCACGCTGTA-GAAAGAATGGGAAATATTTCAAACGAGGGTGGCC
genomic: GAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|86879993|gb|CI340030.1|CI340030
EST:     GAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|29680675|gb|CB676950.1|CB676950
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|88956524|gb|CI092758.1|CI092758
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|89184026|gb|CI046591.1|CI046591
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|88957228|gb|CI095213.1|CI095213
EST:     CACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: CACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|29616239|gb|CB621251.1|CB621251
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|88904274|gb|CI002007.1|CI002007
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|29641724|gb|CB646731.1|CB646731
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|89190777|gb|CI392630.1|CI392630
EST:     AACGCAGAGAATGGAAAAGCACCATGGGAA-GG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: AACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|86414599|gb|CI069002.1|CI069002
EST:     AGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: AGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|29641418|gb|CB646425.1|CB646425
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|58695050|gb|CK083737.1|CK083737
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|58596057|gb|CK006585.1|CK006585
EST:     AGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|29676039|gb|CB672314.1|CB672314
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|86892851|gb|CI312140.1|CI312140
EST:     GGCAACGCCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACG-CAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|88903053|gb|CI088591.1|CI088591
EST:     AAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCACACGAGGCTGGCC
genomic: AAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|86869962|gb|CI316690.1|CI316690
EST:     GGCAACGCAGAGAACGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTA-GAAAGAAT-GGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|38475807|gb|CF959940.1|CF959940
EST:     NGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|88271774|gb|CI387827.1|CI387827
EST:     GCACCAT-GGAAGGG                         GTAAGAGCACCCTGTA-GAAAGAATGGGAGATATTTCAAAGCGAGGCTGGC
genomic: GCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAA-CGAGGCTGGC
EST: gi|33795503|gb|CF323621.1|CF323621
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|38478883|gb|CF963016.1|CF963016
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGNGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATG-GGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGC
EST: gi|86892855|gb|CI312142.1|CI312142
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|58685144|gb|CK073831.1|CK073831
EST:     TGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGATGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|27577797|gb|CB000492.1|CB000492
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAA--G                         G---GAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|86433701|gb|CI094044.1|CI094044
EST:     CCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: CCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
EST: gi|58603030|gb|CK013558.1|CK013558
EST:     GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC
genomic: GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCC

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: 36 (upstream exon), 69 (downstream exon)
Score: 47

GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagcaaat ... tttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCCGATGCCGAGAAGGCATACTACTTATCACAAGGAATCACACCACCCAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgaactctgtacagcacataaattcctcttacgatggtacgttttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCCGATGCCGAGAAGGCATACTACTTATCACAAGGAATCACACCACCCAACT
                            ctcttac  putative branch site (score: 47)
                                            ttttgtctc  putative PPT
                  acataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaatacatatccttatgtaatctgcagttttaaatgttgtagatattcccaacgcatgaactctgtacagcacataaattcctcttacgatggtacgttttgtctcagGTAAGAGCACGCTGTAGGAAAGAATGGGAGATATTTCAAACGAGGCTGGCCGATGCCGAGAAGGCATACTACTTATCACAAGGAATCACACCACCCAACT

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