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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattccatgttgtgttgggttgcccttgtgctatgaatttacgcctttgcctgcactctagtttcagcagttaactctattttttttgtacattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC

Basic information

species Oryza sativa
transcript LOC_Os01g60190.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 2
tgattccatgttgtgttgggttgcccttgtgctatgaatttacgcc--tttgcctgcactctagtttcagcagttaactctattttttttgtacat-taaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC
   |  || |    |   | |||  || || || | |   ||      |||||  | |  ||   ||||     | || || ||| |    ||||| ||  |||||||||| ||||  |||||| ||||||||||||||||||||||||| ||||| ||    || ||||||||||||||||| ||||| ||||||||||| |
ctttctcacgg-acgaaagattgttct-gttctgtcagcataatttgatttgcaggtatactgtcttcatgcactcaccct-tttgtgaaatacatgtattagGGTGCTCCTGAGAAATGGAGACTAGTGAAGGCTCATGGAACAGCTGTGGGTCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCAC

upper sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 2
tgattccatgttgtgttgggttgcccttgtgctatgaatttacgcctttgcctgcactctagtttcagcagttaactctattttttttg---tacat-taaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC
|  |||  |  |  |   | |||  ||      || |||||     |||||  | |  ||   |  |    || |||     ||   ||   ||  | ||  |||| ||||| ||||  |||||| ||||||||||||||||||||||||| || || ||    || ||||||||||||||||| ||||| ||||||||||| |
tctttctcttgtaagaaagattgttctgtcagcat-aatttgt---tttgcaggtatactgtctatatgcttttacttacccttcagtgaaatatgtatattagGGCGCTCCTGAGAAATGGAGACTAGTGAAGGCTCATGGAACAGCTGTGGGCCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCAC

upper sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
tgattccatgttgtgttgggttgcccttgtgctatgaatt-tacgcctttgcctgcactctagtttcagc--agttaactctattttttttgtacattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC
    ||||    |     || | ||  || |  |  ||    |    | |      | | |   ||      | ||||      ||||||| |  | || | ||||||||| ||  |||||||||| || | ||||||||| || ||||| || ||||| |  ||||||||||||||||| || ||||| ||||||||||| |
--cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatcaggatttttttttgtactaca-gGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC

upper sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
tgattccatgttgtgttgggttgcccttgtgctatgaatttacgcctttgcct----gcactctagtttcagcagttaactctattttttttgtacattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC
 |  ||||| ||  ||   |  | |  |||   |   |     ||||  |       | |  || |||  |  |  | | ||    |||||  |   ||| | |||||| || ||  |||||||||| || | ||||||||| || ||||| || ||||| |  |||||||||||||| || || ||||| |||||||||||||
-gtgtccatttttagt--agccgacggtgtttcaaacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttaca-gGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC

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|84117573|gb|CD151340.1|CD151340
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGTATTCGCTCAAGAAT                         GGTTCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|88727473|gb|CI751128.1|CI751128
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58605105|gb|CK033138.1|CK033138
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGTGCTCATGGAACAGCTGTTGG
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAG-GCTCATGGAACAGCTGTTGG
EST: gi|58687704|gb|CK076391.1|CK076391
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTTCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|2312538|gb|C28693.1|C28693
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTNATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|29636841|gb|CB641850.1|CB641850
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|88407542|gb|CI586383.1|CI586383
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|29634606|gb|CB639615.1|CB639615
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58597783|gb|CK008311.1|CK008311
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTTCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|29633640|gb|CB638649.1|CB638649
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|25800076|gb|CA756037.1|CA756037
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58606286|gb|CK034319.1|CK034319
EST:     CAACTGCATCCATGTCCGCC-AGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATGAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: CAACTGCATCCATGTC-GCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58593381|gb|CF991689.1|CF991689
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCGTGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|29614142|gb|CB619155.1|CB619155
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTTCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|29687802|gb|CB684077.1|CB684077
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|87006706|gb|CI285740.1|CI285740
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|33675454|gb|CF303693.1|CF303693
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58691250|gb|CK079937.1|CK079937
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTTCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58670062|gb|CK058748.1|CK058748
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTTCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|29670486|gb|CB666761.1|CB666761
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58667774|gb|CK056460.1|CK056460
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTTCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58610007|gb|CK038040.1|CK038040
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|88762402|gb|CI771958.1|CI771958
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
EST: gi|58690635|gb|CK079322.1|CK079322
EST:     ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAAT                         GGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT
genomic: ACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGT

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: 75 (upstream exon), 74 (downstream exon)
Score: 125

GGTAGCCCTCGTCGTGCTTGACGGATGGGGCGAGGCCAACGCCGACAAGTACAACTGCATCCATGTCGCCCAGACGCCCGTCATGGATTCGCTCAAGAATgtatgcttcc ... acattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgcctgcactctagtttcagcagttaactctattttttttgtacattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC
                        agttaac  putative branch site (score: 125)
                          ttaactctattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattccatgttgtgttgggttgcccttgtgctatgaatttacgcctttgcctgcactctagtttcagcagttaactctattttttttgtacattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - catgttg
- - - - - - - - - - - - -cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - tgcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcagt