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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaacatgatgtcatttatcttttagttttttctttatcatcacccaaatgtatatggttttaaatggtgacatttggcccctaattttgattta...

Basic information

species Oryza sativa
transcript LOC_Os04g32330.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G079538_T03 (Zea mays), 5'ss of exon 9
GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaacatgatgtcatttatcttttagttttttctttatcatcacccaaatgtatatggttttaaatggtgacatt-tggcccctaattttgattta-
||||||||||||||||||||||||||||||||||||||| | |||||||| || ||||| |||||||||||||  ||||||||||||||||||||||||||   |   |   ||||| | || ||||   |   |       |      | | | |  |||  |||  ||  ||| |   |  |     ||  | | 
GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttctcaag--cattttttttctagtagatcgctacagtagatttctgtctgtttattttataattttgctattgtcatcattgcaactgtataaa

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G807639_T02 (Zea mays), 5'ss of exon 9
GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaacatgatgtcatttatcttttagttttttctttatcatcacccaaatgtatatggttttaaatggtgacatt-tggcccctaattttgattta-
||||| ||||||||||||||||||||||||||||||||| | |||||||| || ||||| |||||||||||  | ||||||||||||||||||||||||||   |   |  |  |   ||   ||| ||  |      |||   |  |   | |    |||    |  || |||  | ||  ||   |   ||    
GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttctcaac-tattccttccagtagattgctacagtacat-gtctgatcattttatatttgtgctcttgtcatcgttgcaactgtataaaatggtg

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G46200.1 (Glycine max), 5'ss of exon 11
GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaacatgat-gtca--tttatcttttagttttttctttatcatcacccaaatgtatatggttttaaatggtgacatttggcccctaattttgattta
|| || ||| |||||||  |||| ||  |||| |  ||  |||| ||||| |||||||||||||| |||||||| || || ||||||||||| |||||||||    |||| ||||  ||      |||| ||||  | |  |   | |   |||| | |  |     |||    |||       | | | ||  ||||
GTTCCTATGACAAGGCTTCGGAAACGAGTTGCTACACGGCTGAAAGATTCCCAAAACACATTTGCTATGCTGACTACCTTCAATGAAGTTGATATgtaagttttgttgattgtcaaattgtagcattagattttcatattgctcaagctggatgttttt--tccccgatgtgtgcatcaaaattc-actattacttta

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA14G02530.2 (Glycine max), 5'ss of exon 11
GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaacatgatgtcatttatcttttagttttttctttatcatcacccaaatgtatatggttttaaatggtg-acatttggcccctaattttgattta--
|| || ||| |||||||  |||| ||  |||| |  ||  |||| ||||| |||||||| ||||| |||||||| || || ||||||||||| |||||||||    ||||    |  |  | |    |     ||||  ||  | ||||  | |||| |||||     ||    | |       | | ||   |||  
GTTCCTATGACAAGGCTTCGGAAACGAGTTGCTACACGGCTGAAAGATTCCCAAAACACGTTTGCTATGCTGACAACCTTCAATGAAGTTGATATgtaagttttgttgat--tgtcaaattgtagcataagattttaatattgctcaaac-tgtatgtttttaccccatgtgtgtataaaatgcactattacattatt

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv10s0116g01480.t01 (Vitis vinifera), 5'ss of exon 12
GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaacatgatgtcatttatcttttagttttttctttatcatcacccaaatgtatatggttttaaatggtgacatttggcccctaattttgattta-----
|| || ||| ||||  | ||||| ||| ||||||  |||||||| ||||| |||||||| |||||||||||||||||||| ||||||||||| |||||||||   ||| |    |||   || |  |||  |  |  |||  |        | | |   |  |  |  ||    |  |||  | |||||     |     
GTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttg-tatgttacagtttgaattat--tttgattatagtcagtattatctcatttttttgtccacttaatgtagct--gcctttcattttagccaagtgcc

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|38478516|gb|CF962649.1|CF962649
EST:     GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
EST: gi|33795334|gb|CF323538.1|CF323538
EST:     GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
EST: gi|33794308|gb|CF323041.1|CF323041
EST:     GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
EST: gi|25806798|gb|CA762759.1|CA762759
EST:     GACCACATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: GACCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
EST: gi|11233501|gb|AU164913.1|AU164913
EST:     CCACATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: CCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
EST: gi|5701685|gb|AU062775.2|AU062775
EST:     GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
EST: gi|55435262|gb|CV730762.1|CV730762
EST:     GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
EST: gi|5443721|gb|AU062434.2|AU062434
EST:     GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: GATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
EST: gi|58609985|gb|CK038018.1|CK038018
EST:     ATTCACAAAACACATTTGCAATGCTGACGACGATTTAATGAAGTTGACAT                         GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA
genomic: ATTCACAAAACACATTTGCAATGCTGACCAC-ATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAA

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), 70 (downstream exon)
Score: 90

GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaac ... tacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACATgtaagttaacatgatgtcatttatcttttagttttttctttatcatcacccaaatgtatatggttttaaatggtgacatttggcccctaattttgattta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG