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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGATCCTTTCACGTATCAAAGTACATTTGAATGCACTAAAGAGATACACCTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcgcagtccatgttcatgcatagtacagttcatccactctcttttacatgtttcctggttattactgactcgtttgtttgttgcttctgtaaatatatttcag

Basic information

species Oryza sativa
transcript LOC_Os02g57390.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G123537_T02 (Zea mays), 5'ss of exon 9
TTGATCCTTTCACGTATCAAAGTACATTTGAATGCACTAAAGAGATACACCTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatt--tcgcagtccatgttcatgcatagtacagttcatccactctcttttacatgtttcctggttattactgactcgtttgtttgttgcttctgtaaatatatttcag
||||| ||||| |||||||| || || ||||||||||| || || |||||||||||||| ||||||||  |||| ||||||||||||||||| ||||||||| |||   || ||   |       |  ||| |  |   |||  | ||  | | |  ||    |||    ||      | ||||||     | ||||    ||   ||||||
TTGATTCTTTCCCGTATCAAGGTCCACTTGAATGCACTGAAAAGGTACACCTATGGGAAGCATATTGTGACACGTGTTGAGAAGCTTATTGCCGCAGGAGgtaaatagatcccaagacccaaagctatatactgaaaaccattta-tccttgtcatttgaccactgagcgtttgcattttgtttgt-----gtttcttatcatccttttcag

upper sequence: LOC_Os02g57390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G10360.1 (Arabidopsis thaliana), 5'ss of exon 10
TTGATCCTTTCACGTATCAAAGTACATTTGAATGCACTAAAGAGATACACCTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaat-ttcgcagtccatgttcatgcatagtacagttcat--ccactctcttttacatgtttcctggttattactgactcgtttgtttgttgcttctgtaaatatatttcag
 | || ||||| || ||||||||||| ||||||||  | ||||||||||| ||||||||||| || ||||| |||||||||||||||||  || | |||||| ||  ||     ||  ||| ||   | |  |||||||||   ||   || |  |    | | ||  ||  | | |                                    
CTCATTCTTTCTCGCATCAAAGTACACTTGAATGCCTTGAAGAGATACACATATGGGAAACACATCGTTGCCCGGGTTGAGAAGCTTATCACTACTGGAGgtaaacatttcttctctctgtaca---acatcacagttcatgatcatgatcatgaatcactcttcttctttctgcag------------------------------------

upper sequence: LOC_Os02g57390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv13s0019g04640.t01 (Vitis vinifera), 5'ss of exon 10
TTGATCCTTTCACGTATCAAAGTACATTTGAATGCACTAAAGAGATACACCTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcgcagtccatgttcatgcatagtacagttcatccactctcttttacatgtttcctggttattactgactcgtttgtttgttgcttctgtaaatatatttcag
||||| || || || ||||| || ||| | ||  | || |||||||| || ||||| |||||||||||| | ||||| || ||||| |||||  |||||||||| |  | |  | | |||  || |||  |    ||  |||  | | ||| | |     | |   || || | ||||  |  ||  |   || | |  |          
TTGATTCTCTCTCGCATCAAGGTCCATCTCAACACCCTGAAGAGATATACTTATGGTAAACATATTGTTTCTCGGGTGGAAAAGCTCATTGCAACAGGAGgtgagtaacccttttcctgtaaat-catttt----tttttcctttttttttaaaaaaaaacataactagtaat-actcaatctttaatatattttttgcag---------

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|13420869|gb|AU174959.1|AU174959
EST:     TTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCNATGGTTAGT
genomic: TTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|29675532|gb|CB671807.1|CB671807
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|58688595|gb|CK077282.1|CK077282
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|58592822|gb|CF991130.1|CF991130
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTGCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|58030884|gb|CX728427.1|CX728427
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|27548203|gb|CA766303.2|CA766303
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|29684735|gb|CB681010.1|CB681010
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|86477672|gb|CI120305.1|CI120305
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|89190808|gb|CI392661.1|CI392661
EST:     GAAACATATTGTTGCACGGTTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCCTCATCTTCGTGAGATTCCAATGGTTAGT
genomic: GAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|88989521|gb|CI043936.1|CI043936
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|27920994|gb|CB096802.1|CB096802
EST:     CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: CTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|86834907|gb|CI345991.1|CI345991
EST:     TGAGAAGCTTATTGCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: TGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
EST: gi|88263740|gb|CI366641.1|CI366641
EST:     GAAGCATATTCCTGCAGGAG                         AAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT
genomic: GAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGT

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: 74 (upstream exon), 72 (downstream exon)
Score: 29

TTGATCCTTTCACGTATCAAAGTACATTTGAATGCACTAAAGAGATACACCTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcg ... tatatttcagAAAGGCGCAGTGGAGTGTCTTCGTCATCTTCGTGAGATTGCAATGGTTAGTTTGACAGAATAACACCTGTACAGACAAATAGCGAGGCTAGCCTTACCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGATCCTTTCACGTATCAAAGTACATTTGAATGCACTAAAGAGATACACCTATGGGAAACATATTGTTGCACGGGTTGAGAAGCTTATTGCTGCAGGAGgtgaatttcgcagtccatgttcatgcatagtacagttcatccactctcttttacatgtttcctggttattactgactcgtttgtttgttgcttctgtaaatatatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG