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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtgcacctgtggtggaagcattatgtaattgcatcaaacttcatataggagtactaggatttgctagtgcacttgtgcacacacaatacagag...

Basic information

species Oryza sativa
transcript LOC_Os01g49690.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G518717_T03 (Zea mays), 5'ss of exon 5
GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgtt-gtgcacctgtggtggaagcattatgtaattgcatcaaacttcatataggagtacta--ggatttgctagtgcacttgtgcacacacaatacagag-
|||||||| || || |||||||||||||||||||| ||||| ||||||||| ||||||||  |||||  |||||||||| || |   |||  |  | |    ||||  ||| | ||     || |   |  ||||   |  |    |  | || |        | |||| |  || 
GTGTGGTCTGCACCCAATTATTGCTACAGATGTGGCAATGTAGCTTCTATATTAAGCTTCGATGAGAAGATGgtatgttagttcttttgtcttcaagg----atgtgcttgaagcatttcacacacgtggttacttttgagtcaatttatacaataagtttatctcaatccttagt

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgtt-gtgcacctgtggtggaagcattatgtaattgcatcaaacttcatataggagtactag-gatttgctagtgcacttgtgcacacacaatacagag--
|||||||| || ||||||||||||||||||||||| ||||| ||||||||  ||||||||  |||||  |||||||||  || |   |||  |  ||| ||    ||   |||| | ||   | |   || ||||   || ||   |||  | || | ||   |   ||       
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtc-ttcaaggatctgctagaagcattacac---acacctgattacttttgacttttgagtcaatttatacaataagtttatctcaat

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 9
GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtgcacctgtgg-----tggaagcattatgtaattgcatcaaacttcatataggagtactaggatttgctagtgcacttgtgcacacacaatacagag--------------------------------------------------------------
|||||||||||||| || ||||||||||||||||||||||||||||| ||  |||||||||  || |  |||||| |||    | || ||      |||      |||  ||    ||||  |||  | |  |  |  ||   ||   | |         | ||| |  | |   |                                                               
GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATCTTAAGCTTCAACGAAAATATGgtaggtttcatatctttgacgttctggtcatgatatccaacgctatcattcttgttgttaggat-ttaatgttcctttgcaatgcgacgtacatatcacatgcatgtcaactgacattaatcaagttgacttctgatattgttactgatgtgattctgacatcgcag

upper sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 5'ss of exon 9
GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtgcacctgtggtggaagcattatgtaattgcatcaaacttcatataggagtactaggatttgctagtgcacttgtgcacacacaatacagag--------------------------------------------------------------------------------------------------
|||||||| ||||||||||||||||| |||||||||||||||||||| ||| ||||||||| ||| |  |||||| |||       |    || | ||| |   || ||      |   |  |||   |  ||  | |||||  | |    |||   |  || | |  | |                                                                                                   
GTGTGGTCTGCTCCTAATTATTGCTATAGATGTGGAAATGTTGCTTCGATATTAAGCTTCAATGAAAATATGgtaggtttactgtgttacatgtatgcaatgcttattttatattattattttattttaaaacatgtatttggcaat-tttttgca-atgcaaagtgtatatttcatgtgtgtcagctaatatttattcttaagaagttatttatggaagctaggtttactttgcttcgttttgaagttcgcgtttatgttactttgcag

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|88486727|gb|CI423998.1|CI423998
EST:     GCTACAGATGTGGAAATGTTGCTTCTATAGTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88512520|gb|CI440026.1|CI440026
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88508989|gb|CI436495.1|CI436495
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88989163|gb|CI042276.1|CI042276
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|86253096|gb|CI058021.1|CI058021
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|163921174|gb|EG710163.1|EG710163
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|218484413|gb|FG953190.1|FG953190
EST:     CTACAGATGTGGAAATGTTGCTTCTATACTAAGCCTTC-GTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAA
genomic: CTACAGATGTGGAAATGTTGCTTCTATACTAAGC-TTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAA
EST: gi|88508512|gb|CI436018.1|CI436018
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|86832994|gb|CI333593.1|CI333593
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88560342|gb|CI490996.1|CI490996
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88969389|gb|CI382928.1|CI382928
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88534514|gb|CI463241.1|CI463241
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|86870962|gb|CI326781.1|CI326781
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|89195213|gb|CI051326.1|CI051326
EST:     AATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: AATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88511060|gb|CI438566.1|CI438566
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88486874|gb|CI424145.1|CI424145
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|325493557|gb|JG458081.1|JG458081
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|218492898|gb|FG955355.1|FG955355
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|27577630|gb|CB000325.1|CB000325
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88511102|gb|CI438608.1|CI438608
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|86422413|gb|CI059986.1|CI059986
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88472189|gb|CI409460.1|CI409460
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88380619|gb|CI521188.1|CI521188
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|86419470|gb|CI054271.1|CI054271
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|3767660|gb|AU031687.1|AU031687
EST:     GCTACNGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|51946060|gb|CV152401.1|CV152401
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|86429383|gb|CI076064.1|CI076064
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|89180552|gb|CI044831.1|CI044831
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|29686455|gb|CB682730.1|CB682730
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
EST: gi|88269395|gb|CI380693.1|CI380693
EST:     CTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAAGATGC
genomic: CTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGAC-AATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACC-AGATGC
EST: gi|88505434|gb|CI432940.1|CI432940
EST:     GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATG                         GAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA
genomic: GCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGA

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: 72 (upstream exon), 74 (downstream exon)
Score: 93

GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtg ... aaaacatcagGAAAGAGAGGTCAAATTCTTCACAGAGACAGAGGAGAATAACCAGATGCGAGGACCGAGGACTGCTGTCCCATATTTCCTCTGACTTCATCAATTGTACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgttgtgcacctgtggtggaagcattatgtaattgcatcaaacttcatataggagtactaggatttgctagtgcacttgtgcacacacaatacagag

- - - - - - - - - - - - - CAGATG