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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag

Basic information

species Oryza sativa
transcript LOC_Os06g01390.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G052389_T01 (Zea mays), 5'ss of exon 9
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag
||||||||||||| |||||||||| ||||||||||| ||||||||  |||||||||| ||||||||||| ||||||||||| || |||||||| |||||||||  | | |   | ||  || || |||  |||    || | |   |    ||||| | |            | ||   | || | | ||| |  |  |    |  ||||  ||   |  |||||| |    ||   |||| |   | ||||| |  ||||||
TGGACATGGTTACTTGAACAGCAGTGGGCTTCCTGAGTTGTTTGCGGTCTATGTTCCCGCTTGCACTTACGAAGGAGACAACGTCGTTTTGCTTTTGCAGgtttat-tacccatattccttagtcctgacgatgtcgatcatttatca---tgcttttagc----------acgtaatgtatttgactgaagccaattttttttatttca--ttgtgtgtgttttgtttttgtttttgtca-atggtgtggtgatacctgcag

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 9
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgctattgttgtt-ttgttctgtgg--atactaataact-ctcctacctgcttgtg-gttgtgtg---gatggcctagcttgttgggccgaatcataggtccag----------tccttcaagtttcctcagttttggtcaatt-tacagtcataa----cctttggtgctctctgcag
 ||||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||| |||| ||||||||| ||||| |  || ||    |   |  |     || |  |  || || |||  ||  | || |     ||   ||| |  |  |   || |    |   | ||    ||          | |||    | | |||  |||||| ||||  || ||| |||     ||||||| |    ||||||
CGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTTATGAAGGAGACAATATTGTTCTGCTTTTGCAGgtttgtatgtttctgatggcactagccaataatcgtagttttggctactactagttgagtatgtgcgacatgacagattgtgttccacattagttaaagaaaaagacatagaagatgtttttgcttttcctctactccattttggacaatgatatagtaataggcatcctttgggggaacctgcag

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA01G41600.1 (Glycine max), 5'ss of exon 9
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagt---atgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag
 || |||||||||||    ||||| || || ||||| || |||||| | ||||||||||| ||||| ||||||||||||||| ||||  | || || |||||| ||   | | ||    |||| |    |     |  |||| | | |   |     |  |   |  ||   |  ||     ||||   | | ||   | ||                                                                
CGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGTATGAAGGAGACAATATTGTGCTTCTTTTACAGgtttgttaaaagttaaaaatgttatacaatcattttgttaatcattatttaattcagtctttactaagtcctt--ccacagatgttaa-caggatttaatgtg---------------------------------------------------------------

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA14G14990.1 (Glycine max), 5'ss of exon 8
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagt-atgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttg--ggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag
||| |||||||||||    ||||| || || ||||| || |||||| | ||||||||||| ||||| ||||||||||||||| ||||  | || || |||||| || |    ||     | || | |  |  ||  |  ||||  |  ||  |  ||  |  | |    |   | |     | ||    | | ||   | ||                                                                
TGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGTATGAAGGAGACAATATTGTGCTTCTTTTACAGgtttgttaaaagataaaaatcttatacaatc-attttgttaaccat--tatttaattaagtctttactaagtccttccacggctgttaacaggatttaatgtg---------------------------------------------------------------

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA11G03800.1 (Glycine max), 5'ss of exon 9
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagt-atgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttg--ggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag
||| |||||||||||    ||||| || || ||||| || |||||| | ||||||||||| ||||| ||||||||||||||||||||  | || || |||||| || |    ||     | || | |  |  ||  |  |||   |  ||  |  ||  |  | |    |   | |     | ||    | | ||   | ||                                                                
TGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGTATGAAGGAGACAATGTTGTGCTTCTGTTACAGgtttgttaaaagataaaaatcttatacaatc-attttgttaatcat--tatttaattaagtctttactaagtccttccacagctgttaacaggatttaatgtg---------------------------------------------------------------

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 9
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag
||||||||| ||| ||    |||| ||||| || ||  |||||||| | ||||||||||| ||||| || |||||||||||||||||  ||| ||| |||||   | ||  ||      |  |  || |   |   | | |||    ||  |   |  | |    | |||  | |||| ||| |  |   ||| || |||   ||  |                                                       
TGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACATACGAAGGAGACAATGTTGTGCTGCAATTACAGgt--atttgtcatca--actgcgagctat---tctcacttactagaataaatctgtcagctcaaatagatttcttagcatgtggctcgttatcttatgtc---tctctgg-----------------------------------------------------

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 5'ss of exon 8
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag
||||||||| ||| ||    | || ||||||||||||||||||||| | ||||||||||||||||| || || |||||||||||||| ||||  || |||||     |    || |  | |||   | |   |  ||| ||   |   |   ||   |  |  |    |||||  |      ||    |      |  |   ||  |  | ||||    |       |  || | |||                         
TGGACATGGATACTTGTGGTGTAGTGGGCTTCCTGAATTGTTTGCTGTATATGTTCCTGCTTGCACATACGAGGGAGACAATGTTGTGTTGCAGTTACAGgtattcttaaacttatcttcttgaa-tatcacttttaagaatcatttca--agcccctactctttataatggcaaa------tgaaatggtcttaaaattttgttatatatgttttaaaa----caatggatcttcag-------------------------

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|86906713|gb|CI291165.1|CI291165
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|29681783|gb|CB678058.1|CB678058
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAG
EST: gi|58670583|gb|CK059269.1|CK059269
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|218498819|gb|FG964003.1|FG964003
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|29641670|gb|CB646677.1|CB646677
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|58693078|gb|CK081765.1|CK081765
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|58652726|gb|CK041406.1|CK041406
EST:     AGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: AGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|58598568|gb|CK009096.1|CK009096
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAG
EST: gi|87023655|gb|CI286406.1|CI286406
EST:     ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAG                         GTTGCAAGGCTTTCTAATAGAAGACTGTATCCCAGTTAGCTTCTGGAAAAC
genomic: ATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGG-TTTCTAAT-GAAGACTGTATCCCAGTTAGCTTCTGGAAAAC

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: 75 (upstream exon), 72 (downstream exon)
Score: 62

TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgc ... ctctctgcagGTTGCAAGGTTTCTAATGAAGACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTTATGAAGGAGACAATGTTGTTTTGCTATTGCAGgttagtatgctattgttgttttgttctgtggatactaataactctcctacctgcttgtggttgtgtggatggcctagcttgttgggccgaatcataggtccagtccttcaagtttcctcagttttggtcaatttacagtcataacctttggtgctctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA