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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgtgtttagtaaatttcaatttggatatatcatgataaacatttatttttaaaagcattgtttcgatagcaattagcaccatggacttaactaattaggtttacatttacag

Basic information

species Oryza sativa
transcript LOC_Os03g55280.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55280.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G076885_T01 (Zea mays), 5'ss of exon 7
GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtata----atcgtgtttagtaaatttcaatt--tggatatatcat---gataaacatttatttttaaaagcattgtttcgatagcaattagcaccatggacttaactaattag--gtttacatttacag
||||| || |||||||| |||||||||||||| ||||||||||| ||||| |  |||| ||||  |||||||     ||| |||||    | || || ||    ||   || ||   | |   ||||  || |  | || | ||  |    ||   |    |       |    ||||| |    | |||| |  |||
GTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCCCTGGATGGTAACCGAGGgtatgtatgatcatgtttga-gagttacagttgacagaagcattatctagttgtgcattacttgtgtatagaaatgggtaatgagttgtggataattatatcggcgctaatcatctatatacaatggcag
















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|88245864|gb|CI245713.1|CI245713
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACTAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|86417412|gb|CI031621.1|CI031621
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|86482873|gb|CI125506.1|CI125506
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|87010136|gb|CI279233.1|CI279233
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|89186248|gb|CI262080.1|CI262080
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|5607365|gb|AU076037.1|AU076037
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCNAGATGATANCAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|86258502|gb|CI064855.1|CI064855
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|41881827|gb|BX927612.1|BX927612
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|12404710|gb|AU166311.1|AU166311
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|86491066|gb|CI133699.1|CI133699
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|87029218|gb|CI276486.1|CI276486
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|13805857|gb|AU181226.1|AU181226
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
EST: gi|88974879|gb|CI023150.1|CI023150
EST:     GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGGTAACAAAGG                         GCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA
genomic: GTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAA

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: 68 (upstream exon), 74 (downstream exon)
Score: 36

GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgt ... acatttacagGCTGGACATATTTGTTTGTGGAGATCAAATACGTAAAGGTGCTGCACTCAATGCTGTGCAGATTGCTGAAATGCTACTCAAGTGATTTTCTTTTCTGTAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGGgtataatcgtgtttagtaaatttcaatttggatatatcatgataaacatttatttttaaaagcattgtttcgatagcaattagcaccatggacttaactaattaggtttacatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG