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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcaagcatataattgtccccttgttatatttttaattctccaagggtgaccaggggggaccagaatgctaactaagcattccttgtctgtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG

Basic information

species Oryza sativa
transcript LOC_Os03g16000.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16000.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G046274_T02 (Zea mays), 3'ss of exon 3
---gtgcaagcatataattgtccccttgttatatttttaattctccaagggtgaccaggggggaccagaatgctaactaagcattccttgtctgtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG
     | ||  || |||    |    | ||| |     |          | | |    ||||| |  ||||||| ||||||||  | |||||| ||||||||||||||| | ||||| ||||||||||| |||||||| ||||| ||||||||||||||||||||||| || ||||||||||||| |||||||||||| ||||
actcagtaaaaatgtaaccagcaatcttttagaaaacgagcagatgctagat-atggagggggccgggaatgctgactaagca--cattgtctttcttcacagGTGGCTGCAAATGGTTGGTCTGAAGGTGAATGCAAGGGAAAGGCTGGCTGGTTCCCATCTGCCTACGTAGAGCAGAGGGACAGAGCCCCGGCAAGCAAGG

upper sequence: LOC_Os03g16000.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA01G35400.1 (Glycine max), 3'ss of exon 9
gtgcaagcatataattgtcccctt-gttatatttttaattctccaagggtgaccaggggggaccagaatgctaactaagcattccttgtctgtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG
 ||  |   | |  |    |  |  |||||| | || |||  |||        | |    || | | ||    | ||  | ||   |   |   ||  ||||| |  |||||||| ||||||||||| ||||||||||| || ||||| ||||| || ||||| |||||  ||     |||||     || || || ||| 
ttgtgatatttttttcagacattaagttataatctttattg-ccagtatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA

upper sequence: LOC_Os03g16000.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA09G34950.1 (Glycine max), 3'ss of exon 10
gtgcaagcatataattgtcccctt---gttatatttttaattctccaagggtgaccaggggggaccagaatgctaactaagcattccttgtctgtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG
     | | | |  ||    | ||   |||||| | || |||  ||||       | |    || | | ||  | | ||  | ||   |   |   ||   |||| |  |||||||| ||||||||||| ||||||||||| || ||||| ||||| || ||||| ||||| |||     |||||     || || || ||| 
--atgatcttttttttcagacttttaagttataatctttattg-ccaatatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA

upper sequence: LOC_Os03g16000.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S65_90V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------gtgcaagcatataattgtccccttgttatatttttaattctc-caagggtgaccaggggggac-cagaatgctaactaagcattcct---tgtctgtcttca-cagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG
                                                ||   | |   |||    ||  |  || |  | ||| ||    |   || ||   |   |      |  | |  |    | |  |   ||| | | ||   |||||| |||| | ||||||||| ||||| ||||| | ||| ||||| || ||||| |||||  ||||||||||| ||||||        || ||||| ||||
gtatgcgtacatgaatcgcgttgggatttcaaccaaaatagtcttaaagctgccgtg-gattaataccacgacatctcatcaatgctagttataatgccctctgaaaatgtccgactccaggtggaaactaatagatgtttatgtttggcagGTGTCTCCAAGTGGGTGGTCGGAAGGAGAATGTAGAGGTAAAGCAGGGTGGTTTCCATCATCCTATGTGGAGAAGAGGGGGGCCATTCCTGCAAGCAAGG

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|86496312|gb|CI138945.1|CI138945
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|88243346|gb|CI244468.1|CI244468
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|88508388|gb|CI435894.1|CI435894
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|87010210|gb|CI279307.1|CI279307
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|86483186|gb|CI125819.1|CI125819
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|88260552|gb|CI362845.1|CI362845
EST:     TGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: TGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|86498164|gb|CI140797.1|CI140797
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|29638624|gb|CB643633.1|CB643633
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|44670489|gb|CR283923.1|CR283923
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|88466118|gb|CI519991.1|CI519991
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|86492886|gb|CI135519.1|CI135519
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|86535234|gb|CI175440.1|CI175440
EST:     CTGATGTCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|88510554|gb|CI438060.1|CI438060
EST:     CTGATGGCGAGCTCANTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATCCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|58602171|gb|CK012699.1|CK012699
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|88466301|gb|CI529710.1|CI529710
EST:     ATGTTNTGGTCCGGCAG                         GTGGCTCCCAATGGGTGTTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: ATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|86878104|gb|CI340652.1|CI340652
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|89163416|gb|CI100306.1|CI100306
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|86537560|gb|CI177766.1|CI177766
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
EST: gi|88284735|gb|CI406181.1|CI406181
EST:     CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTNTGGTCCGGCAG                         GTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG
genomic: CTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGG

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: 51 (upstream exon), 51 (downstream exon)
Score: 8

GTAATCCATCCATTCGATGCTCAGGCTGATGGCGAGCTCAGTATTTCCGTGGGAGATTATGTTGTGGTCCGGCAGgtatacatgg ... gtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtgaccaggggggaccagaatgctaactaagcattccttgtctgtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG
                      tgctaac  putative branch site (score: 8)
                                   ttccttgtctgtcttc  putative PPT
                         taactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaagcatataattgtccccttgttatatttttaattctccaagggtgaccaggggggaccagaatgctaactaagcattccttgtctgtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
-tgcaagc
- - - - - - - -tgtcccc
- - - - - - - - - - - - - - - - - - - -ctccaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaatgc