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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcaaatgctcaactggaagttatttttcatatctcatttctagcactgccatcttattcttcaaaacatctgctgattatctgttctacttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC

Basic information

species Oryza sativa
transcript LOC_Os07g36190.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G108285_T01 (Zea mays), 3'ss of exon 3
tcttcaaatgctcaactggaagttatttttcatatctcatttctagcactgccatcttattctt--caaaacatct--gctgattatctgttctacttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC
   | ||||| |    ||    ||      || ||  || |  | |     | ||| |||||||  ||||   | |  | | | ||||  |||||||  | |||||| | || || ||||||||||| |||||| ||||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||||| |||||||
gtattaaatgtttgtttgttt-ttgaacaacacattccaatgtttgtg--actatcctattcttttcaaattgtttttgataagtatc-attctactcgtgcagCAAAGGTCCGCGACAAAGGTTACCTTTCCTTTAGTTTGGACCAATACCTGCTGCAGCCACCCTCTGTACCGTGAGTCTGAGCTTATCCAGGAGAACTACC

upper sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 3
-tcttcaaatgctcaactggaagttatttttcatatctcatttctagcactgccatcttattct--tcaaaacatctgctgattatctgttctacttt-tccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC
 |  | |||   |   ||  | |||   | |    | |||  |||   |||    | ||| | |  ||       |||  |||| | ||||||   |  |  |||||||||||||||||||||| || || ||||| || ||||| ||||| || || |||||||||||||||||||| |||||||||||  | || ||   ||
ttggtgaaaaatt---ctctatgttgcatgtgtattttcaagtctttgactcgtgttttaatttggtctgtttgactga-gattctttgttctttatgatgaagCAACGATCTGCAACAAAGGTAACTTTCCCTCTTGTGTGGACAAACACCTGTTGTAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCC

upper sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
tcttcaaatgctcaactggaagttatttttcatatctcatttctagcactgccatcttattct--tcaaaacatctgctgattatctgttctacttt-tccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC-
       |   |   ||     | || | | || | |||| ||| | |||      ||| | |  ||       |||  ||||   ||||||   |  |  |||||||||||||||| ||||| ||||| ||||| || ||||| ||||| || ||||||||||| ||||||||||| |||||||||||  | || ||   || 
-tggtggaaatttctctatgtatcatgtgt-at-tttcatgtcttggactcgtgctttaatttggtctctttgactga-gattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT

upper sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
tcttcaaatgctcaac-tggaagttatttttcatatctcatttctagcactgccatcttattcttcaaaacatctgctgattatctgttctacttttc----cagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC
    |  |   | | | |  || |  ||  |    | |      |    ||  | ||  | | |   |     || ||||   | | |||| || ||     |||||||| ||   |||||||||||| || || || || ||||| |||||||| |||||||||||||| |||||||| || ||||||||  | || ||    |
--cacgtagctttatcataaaaatggttggttgggttttggcgttg---cttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC

upper sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
tcttcaaatgctcaactggaagttatttt--tcatatctcatttctag-cactgccatcttattcttcaaaacatctgctgattatctgttctacttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC
  ||   ||| |  |  ||| | | |  |  || ||  |  ||  | |    |   |   |       |   ||||||     | ||| |     ||   |||||| | ||    ||||||||||| || |||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||| ||||| ||    |
-gttgctatgat-gatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttct-tctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC

upper sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 3
tcttcaaatgctcaactggaagttatttttcatatctcatttctagcactgccatcttattcttcaaaacatctgctgattatctgttctacttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC
|  |   |  || |          || |  |||   |  |    | ||     |  ||     ||| |   | || |  || |   |  | ||| | |||||| | ||||| |||||||| ||||| ||| | || ||||| ||||| ||||||||||||||||| |||||||| || ||||||||  | || ||    |
ttgtttcaccctgattctatcaagatatagcattctttgtaaacatcagccagaatttgagaatcacatgctgtgttctttctgcatgtttcttgtacagCAAAGGTCTGCCACAAAGGTGACATTCCCTTTGGTGTGGACAAACACCTGCTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATTGATGAGAATGCGC

upper sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S28_399V6.1 (Physcomitrella patens), 3'ss of exon 3
tcttcaaatgctcaactggaagttatttttcatatctcatttctagcactgccatctt--attcttcaaaacatctgctgattat-ctgttctacttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC
        ||      | ||  ||   ||   |   | | ||  ||   || |  |||     |     |  |  |  |  ||||  || | |  | || ||| |||| || || || || || || ||||| || || |||||||||||||| ||||||||||| ||||||||||||||||| |||||  |||| || ||||
--ccaccgtgtatggttagagattggatta-gtgagtgacttgcagggatgtctcctttagacccatggacaaaatcttatttatgttgatattatatttcagAAACGTTCGGCTACGAAAGTGACCTTTCCACTTGTGTGGACCAACACTTGTTGCAGCCATCCACTGTACCGTGAGTCTGAACTTATTGAGGATAAATACC

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|58677529|gb|CK066216.1|CK066216
EST:     GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
genomic: GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
EST: gi|218501677|gb|FG968638.1|FG968638
EST:     GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
genomic: GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
EST: gi|58677196|gb|CK065883.1|CK065883
EST:     GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
genomic: GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
EST: gi|29682817|gb|CB679092.1|CB679092
EST:     GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
genomic: GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
EST: gi|8857118|gb|AU094436.1|AU094436
EST:     GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
genomic: GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
EST: gi|58597346|gb|CK007874.1|CK007874
EST:     GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
genomic: GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
EST: gi|58597292|gb|CK007820.1|CK007820
EST:     GGCTTTCAGGGTTATTCCGGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACA
genomic: GGCTTTCAGTGT-ATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACA
EST: gi|58676998|gb|CK065685.1|CK065685
EST:     GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
genomic: GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
EST: gi|38480944|gb|CF965033.1|CF965033
EST:     GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAG                         CAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC
genomic: GGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGC

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: 74 (upstream exon), 75 (downstream exon)
Score: 110

GCCATCTGATGGAAAAAATCGAATCTGAAAATCTACTTCATAGGGCTTTCAGTGTATTCCTGTTCAACTCAAAATATGAACTCCTACTCCAGgtttggagaa ... acttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcactgccatcttattcttcaaaacatctgctgattatctgttctacttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC
                            tgctgat  putative branch site (score: 110)
                                     tctgttctacttttcc  putative PPT
        atcttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttcaaatgctcaactggaagttatttttcatatctcatttctagcactgccatcttattcttcaaaacatctgctgattatctgttctacttttccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - caaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat