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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG

Basic information

species Oryza sativa
transcript LOC_Os09g39670.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G009940_T02 (Zea mays), 3'ss of exon 4
gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatata-tggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
||||| || |  | |||  | || || | || | |    ||| || |||     |  ||| |    ||  |   | | ||||||||||||||||| |||||| |    |||||| ||||||||||| ||||||||||||||||| |||||||| ||||||||||| ||| ||||| ||
gtatgtaattgctgtgc--tgtgattatgttctacggtctaatttacttt----gttttgaagaaaacctagccacttgttcaatcttgtgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G25050.1 (Glycine max), 3'ss of exon 2
gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttca---atcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
 ||| ||  ||| | | |  ||  ||||   | |      |   |    | |  | |  |     |  |  | |||  || |   || || |  ||||||| ||||||       | |||||||| || ||||||||||| |||||||| ||||| |||||||| || ||  |  | |||
ttat-catttttaaagtatctttattttacatacacaagaactatagcacgagtgcaaagactaattgttttgtataatttatttatttttttatgtacagTTACAACAATTGGTGTGCATATGGCCAATCAAAGCTTGCTAACATTTTACATGCCAATGAACTCGCAAGACGTCTCAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G25070.1 (Glycine max), 3'ss of exon 3
gtatgcaactttta---tgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaat-atatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
  ||||  | ||||   |  |   |       || | | ||| |   |     |    || |||  ||||    | ||   |||  ||    ||| |||||| ||  |  |  |  | |||||||| |||||||||||||| |||||||| ||||| ||||||||||||||  |  |||||
caatgctgcatttaaagttaagcatacagacattattcctgt-agtgttgcgaaggataagtgttttgtatagttcattatgtttgattccttgt-gtacagTTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACATGCCAATGAACTTGCTAGACGTCTTAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G30040.1 (Glycine max), 3'ss of exon 4
gtatgcaacttttatgcactttgttttt---cttttccttgttaacttccttcaaaggaattgtactgtacta-atatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
 | |  ||  | | |  | |||   | |   |  ||      ||     | ||     |||   | |||  |  |||  |  ||   |    | || ||||| ||||||       | |||||||| || ||||||||||| || ||||||||||| |||||||| || ||| |  | |||
-tttttaaaatatctttattttacatatacacaattaagaactatagcacgtctgcaaaatctaattgttttgcataatttatttgcttccttatt-tacagTTACAACAATTGGTGTGCATATGGACAATCAAAGCTTGCTAATATTTTGCATGCCAATGAACTGGCAAGGCGTCTCAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G30060.1 (Glycine max), 3'ss of exon 4
gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaagga--attgtactgtactaat-atatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
|| ||||  |   ||  |   ||      |  | | |||    |   | |||||||  | |||  ||||  | | ||   |||   |    | | ||  || ||| ||         |||||||| || ||||||||||| |||||||| ||||| ||||||||||| ||  |  |||||
gt-tgcatttagaatcaagcatgcaaacgtgattcatgtagtatctatgcaaaggataagtgttttgtataattcatgaagtttgtttccttttggtgtagCTACCACAATTGGCTTGCATATGGACAATCAAAGCTTGCTAACATTTTACATGCCAATGAACTTGCCAGACGTCTTAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G30050.1 (Glycine max), 3'ss of exon 4
-gtatgcaacttt---tatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
 | |   ||  ||    || ||       || || |    ||||| |       ||  |  |||||  || | |  |  |  ||     |  |  || | || ||  |     |  | || ||||| || ||||||||||| |||||||| |||||||||||||| || ||  |  |||||
tgcacttaaagttaagcatacaagcatgattcctgtgtagtgtta-caaagcataagtgttttgtatagttcgatcac-tatttttgcttccttgtgcatagTTATCAGAAATTCTGCGCGTATGGACAATCAAAGCTTGCTAACATTTTACATGCGAATGAACTAGCAAGACGTCTTAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G25080.1 (Glycine max), 3'ss of exon 3
gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCC----ATTGGA--GCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
| |   |   || ||   | | |      |  | | | |    |  ||  |||||||   ||   |    |||| || || ||| |||  || |    ||| |  | |    | |||   ||||||||||| ||||||||||| |||||||| ||||| || |||||| | ||     |||| 
gaaattagaattgataagcat-gcaaacatgattcctatagtgtctctggaaaggaaaaatataatg--gatatttgatt-aattttgctttttttttgtatagTTACCAGAAGTGGCATGCATATGGGCAATCAAAGCTTGCCAACATTTTACATGCCAACGAACTTACAAGACTTCTTAAA

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G30070.1 (Glycine max), 3'ss of exon 3
gtatgcaacttttatgcactttgtttttcttt--tccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaat-cttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
||| | || |   ||  |   | |       |  | | | |    |  ||  | | |||   ||   |   |||||||  || | |  || | |||||||| ||| |        | ||||||||||| ||||||||||| |||||||| ||||| || |||||||| ||     |||| 
gta-gaaattagaattaatcatatgcagacatgattcctatagtgtctctggagatgaaaaatataatgtaaatatatatttgattatttcttttgtacagTTACCAGAAGTGGCGTGCATATGGGCAATCAAAGCTTGCTAACATTTTACATGCCAACGAACTTGCAAGACTTCTTAAA

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G37750.2 (Glycine max), 3'ss of exon 4
gtatgcaactt--ttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
 |    || |     |   |   || ||    || |  |  ||  | ||  | |  ||| |||  ||||    ||  |   |     |  |  ||| ||| |||| |  |    | ||||||||||||||||||||||| |||||||| ||||| ||||||||| | ||  |  | |||
ctggaaaattaaacaagaaatcctgattccagttcctgtagtatttgccgaccagagaagtgttatgtatatttaattatgtttgcttccttgtgttcagTTACAGCAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACATGCAAATGAACTTACAAGACGTCTCAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G30080.2 (Glycine max), 3'ss of exon 4
---------gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
           ||  | | |  | ||||   | ||    || |  |  ||  |  |  |    ||| |||  ||||| | || ||   |   |    || | | ||| ||||||  |    | ||||||||||||||||||||||| |||||||| ||||| ||||||||| | ||  |  | |||
tttcttgaaaaattaagcatgaaagcac---gattcctgttcctgtagtatttatcgactggagaagtgttatgtacaattacat---ttgcttccttgat-ttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACATGCAAATGAACTTACAAGACGTCTCAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G37760.1 (Glycine max), 3'ss of exon 4
gtatgcaacttttatgcactt---tgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatg---gttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
   |  ||   ||| |||           ||| | | | |||    ||  || |  ||| | ||  | | |  || ||     |||   |    || | | ||| ||||||  |    | |||||||||||||||||||| || |||||||| ||||| ||||||||| | ||  |  | |||
---ttgaaaaattaagcatgaaaacacaattcctgttcctgtagtatttattaactggagtagtgttatgcatatttaattacgtttgcttccttgat-ttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTCGCCAACATTTTACATGCAAATGAACTTACAAGACGTCTCAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G25000.1 (Glycine max), 3'ss of exon 4
gtatgcaacttttatgcactttgtttttcttttccttgt----taacttccttcaaaggaattgtactgtacta-atatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
 |||  |     |||  | ||     | |     | ||     ||   |   |  || | ||   |||||  |  |||  |  ||     |  |  ||||||| ||||||         ||||||||||| ||||||||||| |||||||||||| | ||||| ||||| ||  | || |||
atatctataacatatagatttaaacatacaaacacatgaactatagtatgagtgcaaaggat--aactgttttgtataactaatttg-cttcctaatgtacagTTACAACAATTGGCTTGCATATGGGCAATCAAAGCTTGCTAACATTTTGCATTCCAATGAGCTTGCAAGACGTTTCAAG

upper sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0050g00760.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcaactttta-tgcactttgttt--ttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
 | |     |  || |  |   |||||  |  |||||     ||   | | |||||  |     |||   ||    | |  ||   |   |   | |||||||||||     || | |||||||| |||||||||||||| ||| |||||||||| || |||||  | ||  |  | |||
-tctatttttcctaatttatggtgtttagtctttttctcaaatagtattcatcaaataagagaaactcagctttgttttaatttgtttacgaactttacagGTACAATAGGCTTAGTGCATATGGCCAGTCAAAGCTTGCTAACGTTTTGCATGCTAACGAACTATCAAGACGTCTAAAG

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|86828431|gb|CI278560.1|CI278560
EST:     CATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGA                         GTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
genomic: CATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
EST: gi|58677683|gb|CK066370.1|CK066370
EST:     TGTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGA                         GTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
genomic: TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
EST: gi|5003515|gb|AU068664.1|AU068664
EST:     TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGA                         GTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
genomic: TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
EST: gi|5002903|gb|AU068012.1|AU068012
EST:     TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGNCGAGTCGGA                         GTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
genomic: TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA

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: 50

AATCAAATGTGGAAGGAAGAATCGTTAATGTTTCATCAGAGGGGCACAGGTTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
                      tactaat  putative branch site (score: 50)
                      tactaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT