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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG

Basic information

species Oryza sativa
transcript LOC_Os12g10560.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G052713_T02 (Zea mays), 3'ss of exon 1
gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacct--gttcttcccggaatgg-gctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG-
|||| || | ||||| |    ||  |  | |   |  ||    |  ||     ||  ||||  ||||   | |  | |  | |||||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| ||| | ||||||||||| |||||||||||||| ||||||||| 
gtaacgaactcgcatccgatttccccaatactttct-tcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGG

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 1
gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacct--gttcttcccggaatgg-gctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG
|||| || | ||||| |    ||  |  | |   |  ||    |  ||     ||  ||||  ||||   | |  | |  | |||||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| ||| | ||||||||||| |||||||||||||| |||||||||
gtaacgaactcgcatccgatttccccaatactttct-tcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G37730.1 (Glycine max), 3'ss of exon 1
----------------------------------gtaaagatcccgcattcagcctcttctgttcc----ccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG-
                                     |  ||  |      |  |||||| |||||       | | |   |  ||| |||       |  ||||  | | ||     ||||||||| ||||| ||| |||||||  ||||||| ||||| || || ||||| |||||||| || ||||||||||| ||||||||||||||||| |||||| 
gttccttcgttcatcattctattccctctttcgctccataattacaataataatctcttc-gttccaatatttcttttttccattctaaaattcgttttcctcttttccgcat---tcgcagATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGACTCCGAGAAGCACAAGGTCGAATACGAGG

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 1
----gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG
    ||  | |   |  ||||  ||||||  |||||     | |   |  | |  ||   |   | | |               ||||||||| ||||| ||| |||||||  ||||||| ||||| || || ||||| |||||||| || |||||||| || |||||||||||||| || ||||||
gttcgttcataattc-tattc--cctctttcgttccattttttttttcatttttgaatgattgttttcccctttttccgcattcgcagATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggctg-cagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG
       || | |  | |   |  |    ||       |   | |||       |  ||  |||| |       ||   || |||||||| |||||  | || |||||  ||||||| ||||| || || ||||||||||| || || || || || || ||||||||||||||||| ||||||
---gtactctctcgattatgatgattcaatcttgattgcgaggagattgagttgctgactcgttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0023g03340.t01 (Vitis vinifera), 3'ss of exon 1
gtaaagatcccgcattcagcctcttctgttccccccctctc--------------cgcgatctgaaaccgtacctgttctt--cccggaatgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG
|||||  | |  | ||       |||| ||   ||  | |                |  | ||||||   |   | |||||  |||  ||   |  ||||||||| |||||  || |||||||  ||||||| ||||| ||  | |||||||||||||| ||  ||||||| || ||||| ||||||||||| ||||||
gtaaattttcttcttttttttctttctttttttcctttttggatttgatgttgagtggaacctgaaattctgatttttcttttcccacaaattgtggcagATCCGATTCATATTGTTGCAGAACAGGCAGGGAAAGACTCGATTAGCCAAGTACTACGTTCCTTTCGAGGAATCTGAGAAACACAAGGTCGAATACGAG

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ11600 (Selaginella moellendorffii), 3'ss of exon 1
gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG
                  |    |    || | |     |||| | |  || | ||  |    | ||    | |||    ||||||  | ||||||||  |||| ||||| ||||||||||| || || ||||||||||| ||||||||||| ||||| |||||||| ||| || |||| |||
------------------gtgagtggattttcgcttggatccgtgctgagacatcgatcgccgtgtt----ggatg---cgcagATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAG

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ09792 (Selaginella moellendorffii), 3'ss of exon 1
gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggc-tgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG
                          ||         || |   |||| |   |||   |     |  |||   |||    ||||||  | ||||||||  |||| ||||| ||||||||||| || || ||||||||||| ||||||||||| ||||| |||||||| ||| || |||| |||
-------------------------gtgagtggattttcgcttggatccgtg-ccgagacatcgatcgccgtgttggatgcgcagATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAG

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|33669786|gb|CF298025.1|CF298025
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|428995|gb|D25151.1|D25151
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|86899168|gb|CI298074.1|CI298074
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88414379|gb|CI691539.1|CI691539
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|33693746|gb|CF321985.1|CF321985
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|33659105|gb|CF281718.1|CF281718
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|33689089|gb|CF317328.1|CF317328
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|66923463|gb|CX110311.1|CX110311
EST:     CCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88310668|gb|CI672531.1|CI672531
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88352823|gb|CI678848.1|CI678848
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|4881090|gb|AU065389.1|AU065389
EST:     CGCCCCCCAAATCCACGAGCACCAGCGAGTCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CGCCCCCCAAATCCACGAGCACCAGCGA-TCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88353193|gb|CI654459.1|CI654459
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|33663155|gb|CF294122.1|CF294122
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
EST: gi|88307351|gb|CI641991.1|CI641991
EST:     CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG
genomic: CCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAG

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: 71 (upstream exon), 47 (downstream exon)
Score: 9

AAGAACGCATCTTTCCTGCCTTTCCTCCTCCCAAAGCTCCAAATCGCGCCCCGCCCCCCAAATCCACGAGCACCAGCGATCGCCGTCATCCTCCGCCATGgtaaagatcc ... tgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC