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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaaatgctgaatcctgtttatttcaatttggagatcattatgcttttcttgcattaggttcttatacctctgtgataaatattactaatatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGAT

Basic information

species Oryza sativa
transcript LOC_Os12g06810.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G40440.3 (Glycine max), 3'ss of exon 17
gtcaaatgctgaatcctgtttatttcaatttggagatcattatgcttt-----------tcttgcattaggttcttatacctctgtgataaatattactaatatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGAT
         |||||  |||||  ||  |||   || | ||| | ||||           | || |||||   |  | | | | |  |  |  | ||     |||    |||||  || | || ||||||||||| ||||||||||| |||||| | ||||||||  |||| || ||| |||| || |||| | | || ||    || ||| 
---------tgaatgttgttttatttgattcacagttgattttactttgtatgatactatttttcattaaagtaatgtgctttta-gccagctgttcggtttatttc-cagGTGCTGTCTCCTGAAATGAGCTTAGCCACAGTGCGAGCTTATATATGGAAGAAATCAGATGACTTGGTTCTAAATTACAGACTAGTTCAAGGCAGTTGAC

upper sequence: LOC_Os12g06810.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 18
----------------------------gtcaaatgctgaatcctgtttat--ttcaatttggagatcattatgcttttcttgcattaggttcttatacctctgtgataaatattactaatatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGAT
                             |  |||| |  ||    || |   || | ||||         || || || || |||||   |  | | | | |  |  |  | ||     |||    |||||| || | || ||||||||||| ||||||||||| |||||| | ||||||||  |||| || ||| |||| || |||| | | || ||    || ||| 
gttttttgatattgtttggcccaaattgattgaatgttttatttgattcacaattgactttgctttgtgagatactgttttt-cattaaagtaatgtgcattta-gccagctgttcggtttatttc-cagGTTCTGTCTCCTGAAATGAGCTTAGCCACAGTGCGAGCTTATATATGGAAGAAATCAGATGACTTGGTTCTAAATTACAGACTAGTTCAAAGCAGGTGA-

upper sequence: LOC_Os12g06810.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G43070.1 (Glycine max), 3'ss of exon 17
gtcaaatgctgaatcctgtttatttcaatttggagatcattatgcttt-----------tcttgcattaggttcttatacctctgtgataaatattactaatatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGAT
         |||||  |||||  ||  |||   || | ||| | ||||           | || ||||    |  | | | | |  |  |  | ||     |||    |||||  || | || ||||||||||| |||||||| || |||||||| ||||||||  |||| || ||| |||| || |||| | | || ||    || ||| 
---------tgaatgttgttttatttgattcacagttgattttactttgtatgatactgtttttcattgaagtaatgtgctttta-gccagctgtttggtttatttc-cagGTGCTGTCTCCTGAAATGAGCTTAGCCACAGTTCGAGCTTATGTATGGAAGAAATCAGATGACTTGGTTCTAAATTACAGACTAGTTCAAGGCAGGTGA-

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|87027399|gb|CI270074.1|CI270074
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|87005839|gb|CI316258.1|CI316258
EST:     CAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGGTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: CAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|88995547|gb|CI022870.1|CI022870
EST:     AAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|58685416|gb|CK074103.1|CK074103
EST:     AACCATGGCCAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|88840572|gb|CI080026.1|CI080026
EST:     TGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: TGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|86497544|gb|CI140177.1|CI140177
EST:     ACCATGGCAAAAATTGAAACCTTCTGTAGACG-TATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: ACCATGGCAAAAATTGAAACCTTCTGTAGA-GATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|86885229|gb|CI316989.1|CI316989
EST:     TTGTGTAACAGCCAG                         GTTTTGTCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: TTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|86257359|gb|CI004177.1|CI004177
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|27554489|gb|CA998389.1|CA998389
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|86875063|gb|CI322284.1|CI322284
EST:     AACCATGGCAAAAATT-AAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         G-TTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|29666969|gb|CB663244.1|CB663244
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|29683579|gb|CB679854.1|CB679854
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|58600096|gb|CK010624.1|CK010624
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTAGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATG
EST: gi|86477800|gb|CI120433.1|CI120433
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|29670914|gb|CB667189.1|CB667189
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|87017850|gb|CI273872.1|CI273872
EST:     CCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: CCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|88842028|gb|CI081284.1|CI081284
EST:     ACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: ACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|88969566|gb|CI383072.1|CI383072
EST:     AACCTTCTGTAGAGATATTTTGTAACACCCAG                         GTTTTCGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|86481704|gb|CI124337.1|CI124337
EST:     AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG
EST: gi|88960789|gb|CI382470.1|CI382470
EST:     TGTGTAACAGCCAG                         GTTTTGGCACCCGAAATGAGCTTGGCCACAGTCCGGGCTTATGTCTGGAAG
genomic: TGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAG

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: 65 (upstream exon), 75 (downstream exon)
Score: 28

TGGCCAATCACAATTTTCAGCGCTAGATAGTTCTTCACGGCTTGGACTAAAACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... tatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttgcattaggttcttatacctctgtgataaatattactaatatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGAT
                                       tactaat  putative branch site (score: 28)
                             tgataaatattactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaatgctgaatcctgtttatttcaatttggagatcattatgcttttcttgcattaggttcttatacctctgtgataaatattactaatatgaagcagGTTTTGGCACCCGAAATGAGCTTGGCCACAGTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgata