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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagtttcaaatgttgcataattgcttcttttctgaattctgaaccttcctgttttcttggatggcag

Basic information

species Oryza sativa
transcript LOC_Os12g06810.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagtt--------tcaaatgttgcataattgcttcttttctgaattctgaaccttcctgt-tttcttggatggcag
||| ||| |||||||||||||||||||||||||||| || ||||| ||||||||||||||| | ||| ||||||| || ||||||||||||||||| || |||||| || ||        |  | | ||| ||| |  ||    |||    || ||||| ||  ||| || | ||  |  |||
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaattatcttgtgtatattattgaatagtcactgtacttcgtcgttttgaacttttatgtattccctgtgttccag

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G30050.1 (Glycine max), 5'ss of exon 8
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagttt--caaatgttgcataattgcttcttttctgaattc---tga-accttcctgtttt-cttggatggcag---------------------------------------
 || ||| | ||||||||||| || ||||| |||||  | ||||| |||||||||||| |  | ||||||||||||||||||||||| |||||    || ||||||  |||||  | |    |   |||||        | ||||||    |||   || | |||||| |||   | |                                          
ACGCTGTGTGCATTCTTATGCAGTTCATACAGATTCTATTTGGGCTCTTGCAAGCACTTCAACATTTAGTCATGTTTATAGTGGTGGTAGAGACTCTTCTgtgagtgcagtttttcgataaatttttaattatcatgactttgaatttatatgatgtctccttgttttgcttaattagtgaagcttgtgttactgattcgtaattcttttatttttgtag

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA03G40360.1 (Glycine max), 5'ss of exon 9
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagt-caagtttcaaatg--ttgcataattgcttcttttctgaattctgaaccttcctgttttcttggatggcag--------------------------------------------------------------
| ||||| | ||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||  | |||||||||||||||||||| || |||||    || |||||| | |  ||| | |   ||  | |      | |||| |   |  |  | |||    || | |   ||  ||                                                               
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgcgaccttctattaaatttaacatcaaactatttttttgttattacatcttgaatttatgtcacataacatctccttttcttgtttaacttgtgaacctcatcttctaatgttgtattcttttataccctaag

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA03G40440.4 (Glycine max), 5'ss of exon 9
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagtttc-----aaatgttgcat--aattgc-ttcttttctgaattctgaaccttcctgttttcttggatggcag--------------------------------------------------------------
| ||||| | ||||||||||| || ||||| ||||| || ||||| || || ||||| ||  | |||||||||||||||||||| || |||||    || |||||| ||   |      |||  |  |||  || |   || |||| | | | ||  | |||    || | |   ||   |                                                               
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTCGCCAGCACCCCAGCATTTAGTCATGTTTATAGTGGCGGGAGAGACTTTTCAgtgagtgaaaccttctattaaaattaacatcaaactatatttttttattattactacatcttgaacttatgtgacatcatatctccttttcctgtttaacttgtgaacctcatcttctaatgccgtattcttttataccttaag

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA19G43070.1 (Glycine max), 5'ss of exon 9
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagtttc-----aaatgttgcat--aattgcttctt-ttctgaattctgaaccttcctgttttcttggatggcag--------------------------------------------------------------
| ||||| | ||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||  | |||||||||||||||||||| || |||||    || |||||| ||   |       ||  |  |||  || |  || || || | | |  |  | |||    || | |   ||  ||                                                               
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgaaaccttctactgaaattaacatcaaactattttttattattattattacatcttgagtttatgtgaaatcacatctccttttcctgtttaacttgtgaacctcgtcttctaatgtcatattcttttatgccttaag

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA19G42990.1 (Glycine max), 5'ss of exon 9
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagt-caagtttc----aaatgttgcat--aattgcttcttttc-----tgaattctgaacct-----------tcctgttttcttggatggcag------------------------------------------
  ||||| | ||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||  | |||||||||||||||||||| || |||||    || |||||| |||  |||    |||| |  |||  || |  || ||||         ||  ||||  |           ||   ||||||||  |  |                                            
AAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgcaaccttctattaaatttaacatcaaactaattttttttatcatcacatcttgaatttgtcacattacatctccttttcttgtttaactagtgaacctcgtattctaatgttgtattcttttataccctaag

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagtttcaaa--tgttgcataattgcttcttttctgaattctgaaccttcctgttt--tcttggatggcag---------------
||||||| ||||| | ||||| |||||||| ||||| || |||||||||||| |||  || || ||||||||||||||||| ||||||||||| || |  |||||| |     ||||  |||| | |  ||   | || |   |      ||||| | | |||  | |    |  | |               
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagt-agacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 5'ss of exon 9
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagttt------------caaatgttgcataa------ttgcttcttttctgaattctgaaccttcctgttttcttggatggcag-------------------------------------------------------------------------------------------------------
| ||||  | ||||| ||||| |||||||| ||||| |||||||| ||||||||||| ||  | ||||| ||||||||||||||||| || || |  || ||||||  |||||            |||    |||| |        ||| |||||  |   || ||    |   | ||| |||        |                                                                                                       
GAGATGCGTGCATTCCTATGCCGTGCATACAGATTCTGTCTGGGCACTTGCAAGCACCCCAACATTTAGCCATGTTTATAGTGGTGGGAGGGACCTTTCCgtgagtacagttttctcccagaactcaaccaatgcaaatattcccctgcctctttcttatgttttgccattatttttttcctttagcatatgatgttttctcccttttttctttctctatctctctctctctctcttttctgatctttttctgcaatactcatcctttgatgcccaattctgtttatactctcag

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S69_10V6.1 (Physcomitrella patens), 5'ss of exon 9
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagt-----caag-----tttcaaatgttgcata-attgcttcttttctgaattctgaaccttcctgttttcttggatggcag-----------------
 || || |||||||||||||| || ||||| ||||| |||||||| ||||||||||| ||||| || ||||| || |||||||| ||  | ||    || ||  ||     |||        |  | | || |  | ||| |     ||   ||||  || | || ||  ||| | | ||  |                   
ACGCTGCATTCATTCTTATGCAGTTCATACAGATTCTGTCTGGGCTCTTGCAAGCACGCCTTCCTTCAGTCACGTGTATAGTGGCGGTCGTGACTTTTCTgtacgttcctacaaaggcctcctttagtatttcgcagatttcagtgctttcaaattgcgatcattact--tttttagcatcaccaccttacaaatgcccatg

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S28_153V6.1 (Physcomitrella patens), 5'ss of exon 7
---GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGG-AAGAGATCAGTCGgtgagtcaag------tttcaaatgttgcataattgcttcttttctgaattctgaaccttcctgttttcttggatggcag----------------
    || || |||||||||||||| || || | |||||| || ||||| ||||||||||| || || || |||||||| ||||||||| |  |    || ||  ||   | ||        || |    ||      |||    || | |  |   | | | |  |  ||| |     | | |                 
ACAACGTTGCATTCATTCTTATGCGGTTCACATTGATTCTGTTTGGGCCCTTGCAAGCACGCCATCATTCAGTCATGTGTATAGTGGTCGCGACTTCTCTgtaagttctttaaaggactacttaatgcttttggctgttggcagttctgttcacgttaatcatcacaatttacccatcttgtaaatatttgataattaca

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|29678630|gb|CB674905.1|CB674905
EST:     CAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCG                         GTGTACTTGACAGATTTAAGCAATCGAGAGAGTGTCTTGCTCTGCACAAAC
genomic: CAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaag ... tggatggcagGTGTACTTGACAGATTTAAGCAATCGAGAGAGTGTCTTGCTCTGCACAAAC
EST: gi|29670913|gb|CB667188.1|CB667188
EST:     CAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCG                         GTGTACTTGACAGATTTAAGCAATCGAGAGAGTGTCTTGCTCTGCACAAAC
genomic: CAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaag ... tggatggcagGTGTACTTGACAGATTTAAGCAATCGAGAGAGTGTCTTGCTCTGCACAAAC

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: 69 (upstream exon), 73 (downstream exon)
Score: 30

GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaag ... tggatggcagGTGTACTTGACAGATTTAAGCAATCGAGAGAGTGTCTTGCTCTGCACAAACGAGCACCCGATTCTACAATTGTCCTTGCAGGATGATATGATTTGGGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagtttcaaatgttgcataattgcttcttttctgaattctgaaccttcctgttttcttggatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA