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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGGACCATACTTCTGCCAGCCTGTTATCGCTGGACTTGGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatcagttcaattgtgtttttgtttttattcaaattaatttcttttggatctattcatacacatctggatggttatccattgctcatgttctgca...

Basic information

species Oryza sativa
transcript LOC_Os06g43570.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43570.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G092975_T01 (Zea mays), 5'ss of exon 4
ATTTGGACCATACTTCTGCCAGCCTGTTATCGCTGGACTTGGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatcagttcaattgtgtttttgtttttattcaaa--ttaatttcttttggatct---attcatacacatctggatggttatccattgctcatgttctgca
||| || ||||| || |||||||| || || |||||||||||||| ||||| |  |||||||||||||| ||||||||| | ||||||||||| ||||| |||  ||  ||||||  | || | | |    ||  ||| ||||     |   |||  | |   |  || |  |  || |  |   || || |   
ATTCGGGCCATATTTTTGCCAGCCAGTCATTGCTGGACTTGGAGATGACAACGTACCATTTATTTGTACTATGGACTGCTTAGGTGCAAAgtaggtatctgttttatgctgttttcttattgaataagtgcttggtttgttttctgcttgagattattgcgttttagggtcctagtcaa--ggcaatatttt---

upper sequence: LOC_Os06g43570.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G045371_T02 (Zea mays), 5'ss of exon 4
ATTTGGACCATACTTCTGCCAGCCTGTTATCGCTGGACTTGGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatcagttcaattgtgtttttgtttttattcaaa--ttaatttcttttggatct---attcatacacatctggatggttatcca-ttgctcatgttctgca
|||||| ||||| ||||||||||| || || |||||||||||||| ||||| |  ||||| |||||||||||||||||| | ||||||||||| || || ||| | |  ||||||  | || | | ||   ||  ||| ||||     |   |||| | |   | | |||  |  |  | | | || | ||     
ATTTGGGCCATATTTCTGCCAGCCAGTCATTGCTGGACTTGGAGATGACAACGTACCATTCATTTGTACCATGGACTGCCTCGGTGCAAAgtaggtttctgttta-tgttgttttcttcttgaataaatgcttggtttgttttctgcttgagattcttgcgt-tttagatcctagtgaagtcgatctttttg----
















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|88488763|gb|CI426034.1|CI426034
EST:     CATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: CATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|86866304|gb|CI336928.1|CI336928
EST:     GAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATT-GTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCCGAGTCTCTATA
genomic: GAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|86869859|gb|CI316587.1|CI316587
EST:     GGAGAGGACAATGAGCCA-GTATTT-TACCAT-GACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|27578275|gb|CB000970.1|CB000970
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|86887201|gb|CI326016.1|CI326016
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|33658927|gb|CF281540.1|CF281540
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|33663267|gb|CF294234.1|CF294234
EST:     GCATTGGTGCAAA                         GGAACTAGGTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|88270346|gb|CI385604.1|CI385604
EST:     -GAGAGGACAATGAGCCATTTATTTGTACCAT-GACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTT-TATC-GGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|55432675|gb|CV729358.1|CV729358
EST:     AGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: AGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|88519731|gb|CI447385.1|CI447385
EST:     GACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|218483130|gb|FG953131.1|FG953131
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|55413998|gb|CV726374.1|CV726374
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|33684761|gb|CF313000.1|CF313000
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|88510953|gb|CI438459.1|CI438459
EST:     GAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTTTATA
genomic: GAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|88960027|gb|CI381905.1|CI381905
EST:     ACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: ACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|33660368|gb|CF291335.1|CF291335
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|29666365|gb|CB662640.1|CB662640
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|88486810|gb|CI424081.1|CI424081
EST:     ACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: ACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|25806911|gb|CA762872.1|CA762872
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|58683923|gb|CK072610.1|CK072610
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|86420774|gb|CI056763.1|CI056763
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|88835147|gb|CI370450.1|CI370450
EST:     TTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: TTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|33660483|gb|CF291450.1|CF291450
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
EST: gi|33681923|gb|CF310162.1|CF310162
EST:     GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAA                         GGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA
genomic: GGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATA

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), 67 (downstream exon)
Score: 16

ATTTGGACCATACTTCTGCCAGCCTGTTATCGCTGGACTTGGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatca ... ttctgtgcagGGAACTAGCTAAGGATTTCGTTGTATCGGGGACAGCATCGGAGTCTCTATATGGTGCTTGTGAGTCCATGTACAAACCAAACATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGGACCATACTTCTGCCAGCCTGTTATCGCTGGACTTGGAGAGGACAATGAGCCATTTATTTGTACCATGGACTGCATTGGTGCAAAgtatgtatcagttcaattgtgtttttgtttttattcaaattaatttcttttggatctattcatacacatctggatggttatccattgctcatgttctgca

- - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA