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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactccagtctcccctccccagttagcccaatatttttatcaatgcccgtgatgcacacattatattttttcataaagagtgcatttgtttgtactgaacaatggccgtacaaatgcagtctgcttttttgcatgatgctgaatgatacctctgtttatctttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTAC

Basic information

species Oryza sativa
transcript LOC_Os07g10490.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g10490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 10
------------------gtaactccagtctcccctccccagttagcccaatattttta--tcaatgcccgtgatgcacacattatattttttcataaagagtgcatttgtttgtactgaacaatggccgtacaaatgcagtctgcttttttgcatg-atgctgaatgatacctctgtttatctttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTAC
                   |   |     || |  | |  | || |   |    |   |  |       |      | || | | ||   ||  || |||| | | | ||||| | |  ||  ||    || |||||||    ||  ||    |||| ||||| | |||||||  |  |||| ||||||||||||||||| ||| ||| ||||| |||||||| ||| | |||||  | |||||||| ||||| |||||||| |||||||| || |||||||||||||| |||
gtagctgaagtattcactattttttataacttctttacttatttggtttagacctgacaaatttgaatgcacaccacccataatgtaagcttaaatgaagattacttctgtttctgcaaaaagatttttgtgcaaatgcgaattgtattccgccatgcatgctcattgatacccattcttatatttgatgtagACAACTGCAAAGGGCGGTTGGGTTGGATAACCTTTTGTACACGGCGGATGCAGACTTTTCCTGTTTTTCGGACCTTGCTCTCTCATCTCCTGCTGATTAC

upper sequence: LOC_Os07g10490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 10
gtaactccagtctcccctccccagttagcccaatatttttatcaatgcccgtgatgcacacattatattttttcataaagagtgcatttgtttgtactgaacaatggccgtacaaatgcagtctgcttttttgcatgatgctgaatgatac-ctctgtttatctttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTAC
                                 || || | | |||    | | | ||   |  |  |      |||||| |    |   ||||   ||| || |     |  |  |    | || |  ||    |    ||   | || | | ||   |||||       || | ||||   || || ||||| |||||||| |||||||| || || |||||||||||||| || ||| |||||||||||||||||||||| |  || || 
--------------------------------gtaattctctgaattttag-ggtccatgtagaaact------ataaagtg-atgtacttttgctttga-cagttaagattgatctatcctttgatcattattgttcaacttcttcatgcacccttactatctggatgacagGCGACTGGGGAAAGCTGTTGGGTTGGATAACCTTCTCTATACACCCGATGCAGATTTTTCTTGCTTTGCAGACCTTGCACTTTCATCTCCAGAGGATTAT

upper sequence: LOC_Os07g10490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA20G37170.1 (Glycine max), 3'ss of exon 10
gtaactccagtctcccctccccagttagcccaatatttttatcaatgcccgtgatgcacacattatattttttcataaagagtgcatttgtttgtactgaacaatggccgtacaaatgcagtctgcttttttgcatgatgctgaatgatac-ctctgtttatctttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTAC
                       || || |    | |||||     | ||   ||| | | | ||||       |      || | |||| ||  ||  |  || |   |  | | |    | || |  ||    |    ||   | || | | ||   |||||       || | ||||   || || ||||| |||||||| |||||||| || || |||||||||||||| || ||| |||||||||||||||||||||| |  || || 
-----------------------gtaagtctctgaatttta----ggtcc---atgtagaaactata-------aagtgatgtacttttgctttgac--agtaaagattgatcgattttcctttgatcattattgttcaacttcttcatgcacccttactatctgaatgacagGCGACTGGGGAAAGCTGTTGGGTTGGATAACCTTCTCTATACACCCGATGCAGATTTTTCTTGCTTTGCAGACCTTGCACTTTCATCTCCAGAAGATTAT

upper sequence: LOC_Os07g10490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT3G04870.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaactccagtctcccctccccagttagcccaatatttttatcaatgcccgtgatgcacacattatattttttcataaagagtgcatttgtttgtactgaacaatggccgt-acaaatgcagtctgcttttttgcatgatgctgaatgatacctctgtttatctttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTAC
                                                                           |    | |  |      | |  |     |||  ||| |   ||  | ||||  |||| |  | | |     |  |   | |||||         |||| ||  |||||   || |||||||| |||||||||||||||||||| ||||| ||||| || || ||| | || ||||||||  | || ||||| || || 
--------------------------------------------------------------------------gttggtaatctagaatcctatgttttgggatgatcgtgatggatctattctg--ttttggttttaagtc--tttgtttttgtgttttggaaaatcgtagGCAGTTGAAACGAGCGGTTGGCTTAGATAATCTTCTCTACACTCCTGATGCTGATTTCTCGTGCTTTGCGGATCTTGCACTAGCTTCGCCTGCAGATTAT

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|163925596|gb|EG710761.1|EG710761
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
EST: gi|300215694|gb|HO088320.1|HO088320
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
EST: gi|29629811|gb|CB634820.1|CB634820
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
EST: gi|29675444|gb|CB671719.1|CB671719
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTT-GAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
EST: gi|58685253|gb|CK073940.1|CK073940
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
EST: gi|29675446|gb|CB671721.1|CB671721
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTTGAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
EST: gi|4714783|gb|AU055900.1|AU055900
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
EST: gi|8956710|gb|BE230513.1|BE230513
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
EST: gi|29679863|gb|CB676138.1|CB676138
EST:     CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAG                         ACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC
genomic: CTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGC

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: 64 (upstream exon), 73 (downstream exon)
Score: 31

CATTTGACAACATCTACAAGTTAGATGGTGTTCCTGTAGTCACAGTACAGCTTCGTTATAATGGATGGGTTACAGAACTTCAAGATTTGGAGAAATCAAGgtaactccag ... tttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagtctgcttttttgcatgatgctgaatgatacctctgtttatctttgatgtagACAACTGAAAAAGGCAGTTGGCTTGGATAATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTAC
                                            ctttgat  putative branch site (score: 31)
                                 cctctgtttatcttt  CT-rich tract
                                       tttatcttt  TA-rich tract