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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacctttcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatctctgagatttcaggaaatcc...

Basic information

species Oryza sativa
transcript LOC_Os11g43620.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G058252_T03 (Zea mays), 5'ss of exon 1
------------ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacctttcacttcttcttcacttattacatgcttaagccagtgct--tgaaaatt-tcagaatgaaatctctgagatttcaggaaatcc
            || |||||||||||||||||||||||  |||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||| |||||  |||    ||    |||| ||           |||   |  |  |   | |||   ||    || ||| | |||||  | | | |  |    |     
CGTTTTGTGCAGACCGTTCCAGTTAACCCAAAACCTTTTCTGAACAACCTGACAGGAAAGCCTGTTATTGTCAAACTCAAGTGGGGTATGGAGTACAAGGgtaagttatctcctttttgttcagtttaaaccagaacattttgttttccaaatactgccgctgctctttatcaaactgaaaattattatacattcccag----

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G168252_T01 (Zea mays), 5'ss of exon 2
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacctttcacttcttcttcacttattacatgct-taagccagtgcttgaaaat-ttcagaatgaaatctctgagatttca--ggaaatcc----
||||| ||||||||||||||||||||| ||||||||||||| ||||||||||| ||||||||||| |||||||||||||| |||||||||||| ||   | |||  |||   | |   || |  |   ||||  | |  |||||    ||    |  ||  | | |||      | |||| |  | | ||      
ACTGTGCCAGTTAACCCAAAACCTTTCCTGAACAACCTGACGGGGAAGCCTGTAATTGTCAAACTCAAGTGGGGTATGGAGTACAAAGgtaattta---tcttatttttgtatccagtttgaactggaacattttatttgccagatactgcccctgctcttattcaaactgaaaaaattttattgtacatttccag

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G058252_T01 (Zea mays), 5'ss of exon 2
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacctttcacttcttcttcacttattacatgcttaagccagtgct--tgaaaatt-tcagaatgaaatctctgagatttcaggaaatcc
|| |||||||||||||||||||||||  |||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||| |||||  |||    ||    |||| ||           |||   |  |  |   | |||   ||    || ||| | |||||  | | | |  |    |     
ACCGTTCCAGTTAACCCAAAACCTTTTCTGAACAACCTGACAGGAAAGCCTGTTATTGTCAAACTCAAGTGGGGTATGGAGTACAAGGgtaagttatctcctttttgttcagtttaaaccagaacattttgttttccaaatactgccgctgctctttatcaaactgaaaattattatacattcccag----

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G07060.1 (Glycine max), 5'ss of exon 2
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgta---atct-atacttt--tacctttcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatctctgagatttcaggaaatcc
||| | |||||||| || || ||||||||||||||  |||| ||||||||||| ||||| ||||| |||||||| ||||| ||||| ||||    | | || ||||  ||    ||| || |||| |  ||||| ||  ||||  |      ||     ||      |   || | | ||              
ACTATACCAGTTAATCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCTGTAATTGTGAAACTGAAGTGGGGAATGGAGTACAAGGgtatgagtatgatgctttgctatggatcaattgttctactgttattccactcttacactttcatttcgctgttattttgttttatttttcag--------------

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G21250.1 (Glycine max), 5'ss of exon 2
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgta-atctatact--tttacctt---tcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatc-tctgagatttcaggaaatcc-----------------------------
||| ||||||||||||| || ||||||||||||||  |||| |||||||| || ||||| ||||| |||||||| ||||| ||||| ||||   ||||  |  |||    |   ||| || |||| |  ||||| |    |||  |      || |   ||| |   | |  |  |    |||||      |||                              
ACTATTCCAGTTAACCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCCGTAATTGTGAAACTCAAGTGGGGAATGGAGTACAAGGgtatgactatgatgctttgtaatgagtcaattgttctactgttatttccctgttacactttcatttcagtgtttaatcgttagcttgtgcatgatttttttttatcatgtattcactgtgttattttatttttcag

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G30220.1 (Arabidopsis thaliana), 5'ss of exon 2
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacctttcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatctctgagatttcaggaaatcc
||| |||| |||||||| ||||| |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| ||||||||||||||     |||| |||| | |   | | |||      | || | | |  |   |||| ||||  | |  |   ||     |  ||   | ||||        
ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGg-----tatattttt-cttcaaaatgcttt-----tgatgataagtat---ccagagcttatatagct---aacagtcttccttctacttcacag-----

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G30220.2 (Arabidopsis thaliana), 5'ss of exon 2
------------ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacctttcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatctctgagatttcaggaaatcc
            ||| |||| |||||||| ||||| |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| ||||||||||||||     |||| |||| | |   | | |||      | || | | |  |   |||| ||||  | |  |   ||     |  ||   | ||||        
TGTGTTTTGCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGg-----tatattttt-cttcaaaatgcttt-----tgatgataagtat---ccagagcttatatagct---aacagtcttccttctacttcacag-----

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv00s0220g00030.t01 (Vitis vinifera), 5'ss of exon 2
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacctttcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatctctgagatttcaggaaatcc
|| || ||| | ||||| || || |||||||| ||| |||| ||||||||||||||||||||||| |||||||| ||||| |||||||||||   || ||    | ||||   | |  |||| ||   | ||   | |     |  ||   ||  |     ||   | | | ||              
ACCGTACCACTGAACCCTAAGCCCTTCTTGAATAACTTGACTGGGAAGCCTGTCATTGTCAAACTCAAGTGGGGAATGGAGTACAAAGgtaa---attctcccgc-tttcgtctgtggttcaattg--aaatctatgattttttttttcttaacattttcttgggtttttttag--------------

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S46_244V6.1 (Physcomitrella patens), 5'ss of exon 2
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacct---ttcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatctctga-gatttcaggaaatcc--------------------------------------------------------------
||  | || || || || ||||| || |||||| || ||||||||||||| || || || ||||| |||||||| |||||||||||||||  ||| |  | || | |   ||   || |  ||  |||  |   || |      |  |  | |   |||  |  |         |  |||| |    ||| |                                                              
ACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgttttgtttcttgtatttgtttttattttgctttgtttttgttagcaatatggtcttatggttttcgggttttccaggggttgattcctttgaatacatatgtatttgagggtaatacatttaatcgtggcagttgaatgtctggtgtggtgagaacag

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|2442205|gb|C73976.1|C73976
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|86537089|gb|CI177295.1|CI177295
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55439260|gb|CV732933.1|CV732933
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|15846851|gb|BI795127.1|BI795127
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|86418484|gb|CI032693.1|CI032693
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55439258|gb|CV732932.1|CV732932
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|8528391|gb|AU093206.1|AU093206
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|163921024|gb|EG710124.1|EG710124
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|87018205|gb|CI297418.1|CI297418
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55442446|gb|CV734541.1|CV734541
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|426828|gb|D22902.1|D22902
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|117223750|gb|CT842091.1|CT842091
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG

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: 72 (upstream exon), 38 (downstream exon)
Score: 34

ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG




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