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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaaattatatgactgtcaacagatctgttgcactaaaaacctttatgatacttttttgacatgcctctccttttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g05700.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05700.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G166694_T05 (Zea mays), 5'ss of exon 15
AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaaattatatgactgtcaacagatctgttgcactaaaaacctttatgatacttttttgacatgcctctccttttgcag
 || ||||| ||||| || ||||| |||||||||||||||||||| |||||||| |||||||| || ||| |||||||||||||||| || |||||||||||||  ||  || || |     |||  | |  || |||  ||  ||| | | |||   ||||||||||                 
GAAGCACAGGAAGCTGACATGGATTTATTCCTTGGGAACCTGCAACATCAATGCTAAGTTTGATGCTAAACCTATTGAGCTCATTGTTACGACATATCAGgtaatcttggatcatttctgcatcacaaaaaatggtgctatattaacatgtctgacg-ttttttgacag----------------

upper sequence: LOC_Os05g05700.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G166089_T05 (Zea mays), 5'ss of exon 15
AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaaattatatgactgtcaacagatctgttgcactaaaaacctttatgatacttttttgacatgcctctccttttg-cag
||| ||||| ||||| || ||||| |||||||||||||||||||| |||||||| |||||||| || ||| ||||||| || ||||| |||||||||||||||   ||  ||  | |   |||||  | |  || |||  ||  ||||| | ||| | ||||| ||||  |  ||  ||||| |||
AAAGCACAGGAAGCTGACATGGATTTATTCCTTGGGAACCTGCAACATCAATGCTAAGTTTGATGCTAAACCTATTGAACTTATTGTTACAACATATCAGgtagtcttggatcttttctgtgtcacaataaatgctgctatactaacctgtctgacagttttt-gacaaacgacttgttttgacag

upper sequence: LOC_Os05g05700.2 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S169_153V6.1 (Physcomitrella patens), 5'ss of exon 12
AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaaattatatgactgtcaaca-gatctgttgcactaaaaacctttatgatacttttttgacatgcctctccttttgcag----------------
 || ||  | ||  | || ||||| || ||| ||||||| || || || | || ||||||||| || ||  |||||||||| ||||| |||||||||||||||  ||||  | |           ||| ||  ||     || |    |  | |   ||| | |  |  |   |||     |||                  
GAAGCATCGGAAATTGACTTGGATTTACTCCCTGGGAACATGTAACATAACTGGAAAGTTTGATGCCAAGCCTATTGAGCTTATTGTAACAACATATCAGgtaccttta--tcaagccctcagagacacgacatgggttcctgactgtccatgtttgactgtataaaggtcgttcttgaagtgcgcatgtgcttcattctct

upper sequence: LOC_Os05g05700.2 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S177_52V6.1 (Physcomitrella patens), 5'ss of exon 12
AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaaattatatgactgtcaacagatctgtt--gcactaaaaacctttatgat---acttttttgacatgcctctccttttgcag------------
||| ||  | ||||| || |||||||||||||||||||| || || || |  | ||||||||| || ||  |||||||||| |||||||||||||||||||||  || |    |   |       |||  | | ||  | | || ||   || ||  |      || | |   |||   |     ||               
AAAGCATCGGAAGCTGACTTGGATATATTCCTTGGGAACTTGTAACATAACAGGAAAGTTTGACGCTAAGCCTATTGAGCTTATTGTCACAACATATCAGgtactttca--ccaagcgttcagagacatgttttttaagtattacaatttttcatttttgggggttctcggagtgctcgtgtgcctgataaactcagcattt

upper sequence: LOC_Os05g05700.2 (Oryza sativa), 5'ss of exon 15
lower sequence: EFJ25647 (Selaginella moellendorffii), 5'ss of exon 15
AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaaattatatgactgtcaacagatctgttgcactaaaaacctttatgatacttttttgacatgcctctccttttgcag
||| ||||||||||| ||||||||||||||| ||||||| ||||| ||   ||  ||||||||  | ||    || |||||| |||||||||| || ||||| |   ||     ||||   |   ||| | ||        ||| |   |                                   
AAAGCACAGAAAGCTGACCTGGATATATTCCCTGGGAACGTGCAACATTGTTGGGAAGTTTGAACCCAAGCAAATAGAGCTCGTTGTCACAACGTACCAGgtgagcctattgcttatgga-gcatacaaacctaa------aaacatgctcgcag------------------------------

upper sequence: LOC_Os05g05700.2 (Oryza sativa), 5'ss of exon 15
lower sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 15
AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaaattatatgactgtcaacagatctgttgcactaaaaacctttatgatacttttttgacatgcctctccttttgcag
||| ||||||||||| ||||||||||||||| ||||||| ||||| ||   ||  ||||||||  | ||    || |||||| |||||||||| || ||||| |   |      ||||   |   ||| | ||     ||    ||   |                                   
AAAGCACAGAAAGCTGACCTGGATATATTCCCTGGGAACGTGCAACATTGTTGGGAAGTTTGAACCCAAGCAAATAGAGCTCGTTGTCACAACGTACCAGgtgagccttttccttatgga-gcatacaaacctaa-aaacatgcaatgctcgcag------------------------------

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|218486311|gb|FG947934.1|FG947934
EST:     GGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: GGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|218479427|gb|FG960854.1|FG960854
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|29681295|gb|CB677570.1|CB677570
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|88570146|gb|CI661321.1|CI661321
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|218487320|gb|FG963881.1|FG963881
EST:     CAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTA-TCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: CAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|88349830|gb|CI634365.1|CI634365
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCACCGGATCTGACAGGCTTANTTATCCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|29621802|gb|CB626813.1|CB626813
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|88336091|gb|CI647285.1|CI647285
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|218492769|gb|FG946022.1|FG946022
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|313081077|gb|HO213663.1|HO213663
EST:     ACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|33794699|gb|CF323232.1|CF323232
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|218490439|gb|FG950232.1|FG950232
EST:     CAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: CAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
EST: gi|33794279|gb|CF323027.1|CF323027
EST:     ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAG                         GCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG
genomic: ATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAG

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: 48 (upstream exon), 66 (downstream exon)
Score: 155

AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaa ... ccttttgcagGCTGCGTTGCTGCTGCTATTCAACGGATCTGACAGGCTTACTTATTCTGAGATTGTAACACAGCTAAACTTATCAGATGATGATGTAGTGCGTTTGCTCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACACAGAAAGCTTACCTGGATATATTCCTTGGGAACCTGCAATATCAATGCAAAGTTTGAGGCAAAAACTATTGAGCTCATTGTCACAACATATCAGgtaaatttaaattatatgactgtcaacagatctgttgcactaaaaacctttatgatacttttttgacatgcctctccttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA