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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG

Basic information

species Oryza sativa
transcript LOC_Os11g03730.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 2
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
                                               ||   ||  |    | |    ||| ||      |      || ||   | ||      || |||   ||| |    | |   | |||   |    | ||| || | |||||  |  ||| ||   | || |||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||
-----------------------------------------------gtgagacagtgatttct----tggtacacaccagccttattgatc--ttacaaggatttgtccatg-taagcggaatggtccaaacacacttggtcgtgttctca-gataaccaggttg-ctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006130_T06 (Zea mays), 3'ss of exon 2
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
                                                                  |  |||| |  ||| |  | |    | ||| | |  |  |  ||| |   |  |||  ||| ||                |||  || ||| ||  | ||||   || ||||||| |||||||||||||| |||||||| |||||||| || ||||| ||||||||||
-----------------------------------------------------------------gtgaggcagtagtttatcggtagatgctagttcctatgttttaccacatataatcagaaagaata---------------atccaaat-atactg--catggcc--tactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
                                                               |     |  ||| ||||  |   |  ||  | |   | |  |||   |   |  |  |  ||| |   | |   |  |  |  | ||||||| | | ||            |  ||||||| || ||||| || || |||||| ||||||||||||||||||| || ||||
--------------------------------------------------------------ctaaatagaaactattttaatgtaa--ctttacta-gtcatgatgtttaatgtt-ttaatttagctctaataaaatttatga-attctgatgaaattaat------------tacagGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
                                                                      |    ||  ||||| | | ||||| |  ||     |||       |||  | | |   | | ||  | | | |||   ||  | ||| || |||  | |   ||| ||||| ||||||||||| || || |||||| ||||||| ||||||||||| |||||||
----------------------------------------------------------------------gtttgttaatgttacggt-ctcaaatagatc--tttgc-------aatgtacgcaatgtgttcaaat-caatcataaact--ttata-tgctctatgtt--cattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggta--gattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
                                                                     ||   |||    ||  ||      ||    |||      |   |||  |  |  |   |||| |  |  ||   |  |||     ||| ||||   |||        ||||||| |||||||||||||| ||||||||| | ||||| || ||||| || |||||||
--------------------------------------------------------------------gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtt----tga-aatgtctttg--------tgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG

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|88763952|gb|CI773368.1|CI773368
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29673416|gb|CB669691.1|CB669691
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29628283|gb|CB633294.1|CB633294
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29632559|gb|CB637568.1|CB637568
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88734903|gb|CI758411.1|CI758411
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88740536|gb|CI764044.1|CI764044
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29638131|gb|CB643140.1|CB643140
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88745225|gb|CI768585.1|CI768585
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88735131|gb|CI758639.1|CI758639
EST:     CGNAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29680212|gb|CB676487.1|CB676487
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29674874|gb|CB671149.1|CB671149
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|29634180|gb|CB639189.1|CB639189
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST: gi|88737430|gb|CI760938.1|CI760938
EST:     CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAG                         GAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtg ... aatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
                                         ggctaat  putative branch site (score: 3)
                                            taatattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA