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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAGAGGACCAATGTGCTTCTCCTTGGAGATCACATTGGCGACCTTGGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagacttccttatcatcttgctttttgcttaccatttttagatttatcttctgctgcatctatagcttagtttatccccatggatctagactgta...

Basic information

species Oryza sativa
transcript LOC_Os03g44660.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g44660.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G157310_T02 (Zea mays), 5'ss of exon 7
TGAAGAAGAGGACCAATGTGCTTCTCCTTGGAGATCACATTGGCGACCTTGGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagacttccttatcatcttgctttttgcttaccatttttagatttatcttct----gctgcatctatagcttagtttatccccatgg-atctagactgta
||||||| |||||||||||||| || ||||| ||||||||||| ||| | || |||||||||||| |||||||||| |||||||| ||||||||||| |||| |||| ||||  | |    |||| ||  | |  |  |    |    ||| | |||     || |   | |   |||  || | |  | |  |  ||  |    
TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagta-actttttgactgccttgattcattcaaagtagcagtgatattaccatcttgggactaccatttttttttaaattctgcttaagtcaattaagc----

upper sequence: LOC_Os03g44660.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA20G33690.1 (Glycine max), 5'ss of exon 8
TGAAGAAGAGGACCAATGTGCTTCTCCTTGGAGATCACATTGGCGACCTTGGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagacttccttatcatcttgctttttgcttaccatttttagatttatcttctgctgcatctatagcttagtttatccccatggatctag-actgta-
|||||||||| |||||||| || ||||| || ||||||| ||| ||| | ||||||||||||||| | || ||||| |   | ||  |  | ||||| ||||||||       ||  |   |    || |    | | | ||      ||   |    |   ||  |||     | | | |   ||  |  ||    || | 
TGAAGAAGAGAACCAATGTTCTCCTCCTCGGTGATCACACTGGAGACTTGGGAATGTCTGATGGTTTGAATTATGAGACTCGAATATCCATGGGATTCCTgtaagttacgaatctctttgccaaatttatgttcttctaatt----gcttgggtaacacgtaattaatacagaggctcaactgtataaaattattgttgcag

upper sequence: LOC_Os03g44660.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv13s0073g00650.t01 (Vitis vinifera), 5'ss of exon 8
TGAAGAAGAGGACCAATGTGCTTCTCCTTGGAGATCACATTGGCGACCTTGGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagacttccttatcatcttgctttttgcttaccatttttagatttatcttctgctgcatctatagcttagtt-tatccccatggatctagactgta
|||||||||| ||||||||||| || ||||| ||||||||||| ||| | |||||||| |||||| |  |||||||||   | ||  |||| ||||| ||||||||    |    | |  ||   ||   |   ||   || |||    |   || |  |   |||    || |  | |||||  |||     | |   | 
TGAAGAAGAGAACCAATGTGCTGCTTCTTGGTGATCACATTGGAGACTTGGGAATGTCAGATGGTTTGGACTATGAAACTCGAATATCTGTGGGATTCCTgtaagttagttagactttgctcgatctccatatctaatcttattattgctga-ttttaatatttctcctcctaaaatatatccttatgttataacaacttg

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|163921168|gb|EG710157.1|EG710157
EST:     GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGC--TTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|163927859|gb|EG714239.1|EG714239
EST:     GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|88557502|gb|CI487915.1|CI487915
EST:     GATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|33685189|gb|CF313428.1|CF313428
EST:     GGAATGTCTGATGGTCTAAACTATGAAA-CAGGATTGCTGTTGGATTTCT                         GAACA-CAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|88545586|gb|CI475155.1|CI475155
EST:     GGAATGTCTGATGGTCTAAACTATGAANACACGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|163920287|gb|EG709539.1|EG709539
EST:     GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGC--TTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|88830004|gb|CI074676.1|CI074676
EST:     GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|88551563|gb|CI481630.1|CI481630
EST:     AATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: AATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|25806219|gb|CA762180.1|CA762180
EST:     GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|88839839|gb|CI017604.1|CI017604
EST:     CAGGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: CAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|86498135|gb|CI140768.1|CI140768
EST:     GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTTTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|86864180|gb|CI334017.1|CI334017
EST:     GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: GGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
EST: gi|88556421|gb|CI486745.1|CI486745
EST:     TCTGATGGTCTAAACTATGGAAACAGGATTGCTGTTGGATTTCT                         GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT
genomic: TCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATAT

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), 61 (downstream exon)
Score: 17

TGAAGAAGAGGACCAATGTGCTTCTCCTTGGAGATCACATTGGCGACCTTGGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagac ... tgtttcacagGAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAGAGGACCAATGTGCTTCTCCTTGGAGATCACATTGGCGACCTTGGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagacttccttatcatcttgctttttgcttaccatttttagatttatcttctgctgcatctatagcttagtttatccccatggatctagactgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT