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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatgctgttacagtattatactgttatgctctttcatcaagtgtggaatttaatgcacaaacatcaatttttcctattactgtatttcag

Basic information

species Oryza sativa
transcript LOC_Os04g58620.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA07G08030.1 (Glycine max), 5'ss of exon 18
GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagca--atgctgttacagtat-tatactgtt---atgctctttcatcaagtgtggaatttaatgcacaaacatcaatttttcctattactgtatttcag
|||||||| |||||||||||||||||||| ||  | || || || || ||||| |||||||  |  ||| | ||  || |  |||| |||    |||  ||||         | | |||| ||  |  |   |||  |  |  ||  |      || | 
GTTGTCCCAGAGACCTTGGAACCAAGTCTTCAACTAGCAGCCGCCGTGCTTGCTCAGgtaactatcatgttatttgagcagatatattgtccgaatgaactttttaacgtcttagcattttat-tattactctcacctgatgataacaacaccattta-

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA09G39770.1 (Glycine max), 5'ss of exon 22
GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatgctgttacagtattatactgttatgctctttcatcaagtgtggaatttaatgcacaaacatcaatttttcctatt-actgtatttcag--------
|||||||| |||||||||||||||||||| ||  | || |||||||| ||| | |||||||  | |    ||  | ||| ||| |  | ||       |   | | | || | ||||| | | |  |   | | ||  | | |   |||||  |        
GTTGTCCCAGAGACCTTGGAACCAAGTCTTCAACTAGCAGCTGCTGTGCTTTCTCAGgtaacaattatcattg-aatatcatatttctgtgggaacaga---aatattga-tataatggaaatattttggtatgtctcactcataatatttatgtttaatag

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 19
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 5'ss of exon 19
GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatgctgttacagtattatactgttatgctctttcatcaagtgtggaatttaatgcacaaacatcaatttttcctattactgtatttcag
|||||||| |||||  |||| || ||||| |||||||| |||||||||||||| |||||||   ||        | | ||    | ||  | |     |  ||   |  |    | || |  | |||    ||||    ||     || ||||
GTTGTCCCGGAGACTCTGGAGCCTAGTCTACAGTTGGCAGCTGCTGTTCTTGCTCAGgtaaaacata-------aatgtttccttatttagttgaagtagtaatcctaaa---cagtgtatgatcat----tttttgggttgaaacatgtcag

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 19
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 18
GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatgctgttacagtattatactgttatgctctttcatcaagtgtggaatttaatgcacaaacatcaatttttcctattactgtatttcag
||||| ||||||||  ||||||||||||| ||||| || |||||||||||||||||||||    |     ||   ||| |      ||| |     ||| |||   ||  ||||   | |      | ||  ||  |   | || |  |||||
GTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAGgtacaagagataattcttgtagt----cattaag-----tcaccaacaatgttatttggggtat--ttgttaaacttgtcggcttcttt--ttcag

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 17
GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatgctgttacagtattatactgttatgctctttcatcaagtgtggaatttaatgcacaaacatcaattt---ttcctattactg----tatttcag
||||| || |||||||||||||||||||| ||||| ||||||||||||||||||||||||| ||      ||||      ||  | |||   | ||  ||      |  ||  | ||| | || ||  | |||   | |  |  | |      |||||  
GTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAGgtaaacagaatcattacccctcaatcatatta-aatattctattgctaatttaaactgatggaaaatcaggattttagatcctcaacattaaaaccatttc--

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|163927597|gb|EG709981.1|EG709981
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88491733|gb|CI429005.1|CI429005
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|29675208|gb|CB671483.1|CB671483
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|86600893|gb|CI356650.1|CI356650
EST:     ACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: ACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|12622483|gb|AU172696.1|AU172696
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|25806037|gb|CA761998.1|CA761998
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|29630179|gb|CB635188.1|CB635188
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88507019|gb|CI434525.1|CI434525
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|29674001|gb|CB670276.1|CB670276
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|2428987|gb|C73450.1|C73450
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88258892|gb|CI359282.1|CI359282
EST:     CCAGTTGGCTGGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CCAGTTGGCT-GCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88247369|gb|CI247218.1|CI247218
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|86430204|gb|CI082627.1|CI082627
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88502339|gb|CI429845.1|CI429845
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88512671|gb|CI440177.1|CI440177
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88503768|gb|CI431274.1|CI431274
EST:     TCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: TCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|86430421|gb|CI082844.1|CI082844
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88479417|gb|CI416688.1|CI416688
EST:     TGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: TGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
EST: gi|88504559|gb|CI432065.1|CI432065
EST:     CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG                         GCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC
genomic: CTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAAC

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: 65 (upstream exon), 62 (downstream exon)
Score: 39

GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatg ... tgtatttcagGCAAAACTCCCAATGTCAGAGATTGCAGCAACTGTCAATGAGTTCAGGAACCGTCATCTGTCAGAGCTCACAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAGgtaagcaatgctgttacagtattatactgttatgctctttcatcaagtgtggaatttaatgcacaaacatcaatttttcctattactgtatttcag

- - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - GCTGTT