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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGCCCTGTGGGGAAAGCTGGCAGCCGAGATTTTGATGCAGAACTGGGATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctgaatgactatatcacttgttgtggttggttaggtgctttacctaactatttttttaggggaatcacataactaattttgttcctttttttattctcccag

Basic information

species Oryza sativa
transcript LOC_Os07g12110.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12110.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G33770.1 (Glycine max), 5'ss of exon 3
GAGTGCCCTGTGGGGAAAGCTGGCAGCCGAGATTTTGATGCAGAACTGGGATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctgaatgactatatcacttgttgtggttggttaggtgctttacctaactatt--tttttaggggaatcacataactaattttgttcctttttttattctcccag----------------------
||||||  ||||||| ||||||||||| || ||||||||||||||||||||  |||| || || |||||||| || |||||||| || |||||||||||||||   ||   |    |  |   |  |||  || | |        ||   |  |  ||  | ||| | | |    |||       ||||||    ||  |||  |   |                       
GAGTGCATTGTGGGGGAAGCTGGCAGCTGAAATTTTGATGCAGAACTGGGACATTGCTCTTGAAGAGCTCAATCGCTTGAAGGAAATCATTGATTCAAAGgttgttcttgtttgtca-gttgatctttggagtagatgcatgttcttgtttgtcagttgatctttggagtagatgcatgttcttgtttgttatgcttaatatattaatatagactggtgaacttcgttgcag

upper sequence: LOC_Os07g12110.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G16090.1 (Glycine max), 5'ss of exon 3
GAGTGCCCTGTGGGGAAAGCTGGCAGCCGAGATTTTGATGCAGAACTGGGATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctgaatgactatatcacttgttgtggttggttaggtgctttacctaactatttttttaggggaatcacata-actaattttgttcctttttttattctcccag
||||||  ||||||| ||||||||||| || ||||||||||||||||||||  | || || || ||||||||||| |||||||| || ||||| |||||||||   ||   |    |  |   |  ||| |  | | |   || | |   |   | |  ||  |      | | ||| |||  |  ||  | || ||  |         
GAGTGCATTGTGGGGGAAGCTGGCAGCTGAAATTTTGATGCAGAACTGGGACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttgtttgtca-gttggtctttg-gagtagatgcatgttcttgtttgttgtgctta-aaatatttaatatagactggtggtgaactttgttgcag--------

upper sequence: LOC_Os07g12110.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 5'ss of exon 3
GAGTGCCCTGTGGGGAAAGCTGGCAGCCGAGATTTTGATGCAGAACTGGGATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctgaatgactatatcacttgttgtggttggttaggtgctttacctaactatttttttaggggaatcacataactaattttgttcctttttttattctcccag
||||||| ||||||||||||| ||| | || || |||||||| ||||||||| |||| || || ||||| |||||| | || ||||||||||| |||||||||      | |   || |  |||| || | ||| |   |    || |  | | |||   | |  | | || | ||    | |    ||  |||||| |         
GAGTGCCTTGTGGGGAAAGCTCGCATCTGAAATATTGATGCAAAACTGGGATATTGCTCTTGAAGAGCTTAACCGTCTCAAAGAGATTATTGACTCAAAGgtt------agtatttaaa--acttcttctagtttgc--gacctttgaaatcaatatagatgtgagagtat-atatgctaactaccatttgttttttcag--------

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|38471465|gb|CF955596.1|CF955596
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|218479043|gb|FG955974.1|FG955974
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|29688863|gb|CB685138.1|CB685138
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|58657959|gb|CK046639.1|CK046639
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCA
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCA
EST: gi|29630664|gb|CB635673.1|CB635673
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|29617589|gb|CB622601.1|CB622601
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|33794207|gb|CF322994.1|CF322994
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|218481869|gb|FG961133.1|FG961133
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|58687118|gb|CK075805.1|CK075805
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGC
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGC
EST: gi|58671192|gb|CK059878.1|CK059878
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|218501745|gb|FG957162.1|FG957162
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|33795947|gb|CF323841.1|CF323841
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|33677618|gb|CF305857.1|CF305857
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|58694550|gb|CK083237.1|CK083237
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|29682305|gb|CB678580.1|CB678580
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|29628320|gb|CB633331.1|CB633331
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|29645460|gb|CB650467.1|CB650467
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|33794202|gb|CF322991.1|CF322991
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATTTTCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|218491612|gb|FG958894.1|FG958894
EST:     CAACCGTTTAAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: CAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
EST: gi|117243527|gb|CT843109.1|CT843109
EST:     ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAG                         AACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT
genomic: ATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCAT

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), 75 (downstream exon)
Score: 64

GAGTGCCCTGTGGGGAAAGCTGGCAGCCGAGATTTTGATGCAGAACTGGGATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctga ... attctcccagAACTTCTCATCACCACTAAATCAGCTCCAGAATAGGATATGGCTGATGCATTGGAGTATTTTTATCTTCTTTAACCATGAAAACGGCAGAAATGGGATCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGCCCTGTGGGGAAAGCTGGCAGCCGAGATTTTGATGCAGAACTGGGATGTTGCACTGGATGAGCTCAACCGTTTGAAGGAGATTATTGATTCAAAGgtttggctgaatgactatatcacttgttgtggttggttaggtgctttacctaactatttttttaggggaatcacataactaattttgttcctttttttattctcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT