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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatatcgacctatcctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g10070.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 15
gttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatat-cgacctatcctc--tttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
||  ||||| || ||  |||  |   |   ||   |  |  ||  |  |  |  |||| || |||     | |   || ||| | |||||||| ||||| || |||||||| |||||||||||||| || |||
gtccgtctagatcctctctgtctaattgcatttgctttc-ttgagttgaacgattttagatacgatactccgtacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 17
gttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatatcgacctatcctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
||  ||||  |  ||  ||   |   |   || | |  |      |||| |   || | |   |  ||| |  || ||||| |||||||| |||||||| || ||||| |||||||||||||| || |||
gtccgtctggaacctttctatctaattgcatttactttcttgagttcaacaattttaaaaataa--tattccgttgcagGTGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 2
gttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatatcgacctatcctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
||  ||||  |  ||   |   |   |   || | |     ||  |  |  || |||| ||  |    |    || ||||| |||||||||||||||||||| |||||||||||||||||||| ||||||
gtccgtctggaacctt-ttatctaatttcatttactttt-ttgagttgaacggttttaaatgtaatc-tttggttacagGTGTCCAAGTTGTATGAAGTTGTACCTCCTATCCTCACTGAGCTGGGCAAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 16
--gttagtctaaattctagctgcatggctctcttcagtccc----actgtctcaat----aggatttatatcgacctatcc--tctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
    |  | |   ||||   | |     ||| ||| || |     | | | |||||    || |  ||     | |  |||     |  |||| || ||| | |||||||||||||||||| | |||||||||||||| |||
gtactttttttctttctcttttctcttttctgttcggttctcaaaattctatcaatgttcagtagctaacaaaatccttccaactctgtagGTGTCAAAGCTTTATGAAGTTGTGCCTCCTGTTCTCACTGAGCTTGGAAAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 16
---gttagtctaaattctagctg----catggctctcttcagtcccactgtctcaataggatttatatcgaccta---tcctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
    ||| |  ||   ||   |     ||  | | | || | |       ||    |     ||     ||| |    | |  || ||||| || ||| | |||||||| ||||||||||| || |||||||||||||||
gttattacttaaagccctgattaaagacaatggtttgtttatttttgtgttccagttcatccttgagctgacttggtttaccattacagGTTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG

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|88825933|gb|CI776498.1|CI776498
EST:     AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
genomic: AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... cctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
EST: gi|58695418|gb|CK084105.1|CK084105
EST:     AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTG
genomic: AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... cctctttcagGTCTCCAAGTTGTATGAAGTTG
EST: gi|33794400|gb|CF323084.1|CF323084
EST:     AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAG
genomic: AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... cctctttcagGTCTCCAAGTTGTATGAAG
EST: gi|58608873|gb|CK036906.1|CK036906
EST:     AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
genomic: AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... cctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
EST: gi|87021334|gb|CI295393.1|CI295393
EST:     GAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
genomic: GAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... cctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
EST: gi|58694362|gb|CK083049.1|CK083049
EST:     AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
genomic: AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... cctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
EST: gi|38481573|gb|CF965662.1|CF965662
EST:     AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
genomic: AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... cctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG

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: 66 (upstream exon), 42 (downstream exon)
Score: 40

TGGCTTTGGTCATGGAGTTCTACGTAAGACCGATCCACGGTATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... cctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctcttcagtcccactgtctcaataggatttatatcgacctatcctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG
                                        cctatcctctttc  CT-rich tract
                       aataggatttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatatcgacctatcctctttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT