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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_Os11g43620.2
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|87018205|gb|CI297418.1|CI297418
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|86418484|gb|CI032693.1|CI032693
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|117223750|gb|CT842091.1|CT842091
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|86537089|gb|CI177295.1|CI177295
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55442446|gb|CV734541.1|CV734541
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55439258|gb|CV732932.1|CV732932
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55439260|gb|CV732933.1|CV732933
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|8528391|gb|AU093206.1|AU093206
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|15846851|gb|BI795127.1|BI795127
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|163921024|gb|EG710124.1|EG710124
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG