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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtttggaattgcattaatacaatttttgaacgtgaatgcactagtctactacatgtgaagcaccagcactgacacttctatcatttgaactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAG

Basic information

species Oryza sativa
transcript LOC_Os05g15370.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 1
ttagtttggaattgcattaatacaatttttgaacgtgaatgcactagtctac-tacatgtgaagcacca--gcactgacacttctatcatttgaactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAG
   ||  |   | ||  |  |     || |||| ||| |    ||  || |  |  |||| ||| || |  | | |  ||||| |    |||||  || ||||||||||||||||||| |||||||||||| ||||||||| ||| ||||||| |||||||| || ||||| |||
cctgtgggtgctcgc-ctgctcgttcttctgaatgtgcagt--ctgatccatgttgatgtcaagtactactgtattagcacttatggtttttgatgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G163473_T01 (Zea mays), 3'ss of exon 1
-ttagtttggaattgcattaatacaatttttgaacgtgaatgcactagtctactacatgtgaagcaccagcactgacacttctatcattt--gaactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAG
   | | |  | ||     |||   |||| ||||   | | |  |   ||   | || || ||| || |||||||||  ||   || |||  ||  |||||||||||||||||||||| ||||||||||||||||||||||  |  ||||||| |||||||| || ||||| |||
cagaatctctagttatgg-aatgttatttctgaatccgca-gttcacatcatgttca-gtcaagtactagcactgacggttgcttcctttttgatatgtgcagAAAGCACTTGCAGGTCTGAGAAGAATCAATTTAGATGGGCTTCGATGGCGCGTATTTGATGCTAAGGGTCAG

upper sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 1
--ttagtttggaattgcattaatacaatttttgaacgtgaatgcactagtctactacatgtgaagcaccagcactgacacttctatcatttgaact--gtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAG
   |  ||||||  | ||| || | |||| |  |   | | |   ||| | |  |  |  ||      ||| | |   |  |  | | ||  | ||   |||||||||||||||| ||  ||||| |||||||||| || || ||| ||||||| |||||||| || || ||||||
gggttatttggagat-catgaa-aaaattctaaagttttatttgcctaatttgatttagatgctctgtcagtaatagaa--tgcacccttaaatcttcatgcagAAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAG

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|88766306|gb|CI775396.1|CI775396
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88824997|gb|CI775562.1|CI775562
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88743925|gb|CI765361.1|CI765361
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88731413|gb|CI755026.1|CI755026
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88827411|gb|CI777976.1|CI777976
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88364517|gb|CI644595.1|CI644595
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|218498131|gb|FG955911.1|FG955911
EST:     CGCCGTCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: CGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88737104|gb|CI760612.1|CI760612
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88737516|gb|CI759397.1|CI759397
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88572205|gb|CI663776.1|CI663776
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88733819|gb|CI755405.1|CI755405
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|8860173|gb|AU097491.1|AU097491
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|33655563|gb|CF278177.1|CF278177
EST:     TCGCCTCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|33656314|gb|CF278928.1|CF278928
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88724395|gb|CI747654.1|CI747654
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|38477035|gb|CF961168.1|CF961168
EST:     CACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: CACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
EST: gi|88336313|gb|CI648900.1|CI648900
EST:     TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATG                         AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT
genomic: TCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGT

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: 67 (upstream exon), 72 (downstream exon)
Score: 73

CTCTCCTCTCATCGCTCCTCCACCGTCGCCGCCGCCGCCACCGCAGCGGAGCAACCACAGCAGGCGAGCGACATGgtaagatcct ... aactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctactacatgtgaagcaccagcactgacacttctatcatttgaactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAG
                        cactgac  putative branch site (score: 73)
                                    tatcattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtttggaattgcattaatacaatttttgaacgtgaatgcactagtctactacatgtgaagcaccagcactgacacttctatcatttgaactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - -ttgcatt
- - - - - - - - - - - - - - - - - -tgaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccagcac