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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaagatgcatatagaattcacttttcatttgttgtaatgttttagttgtaaatgtaataaacgtattggtctatcatgtatccataacaatatgctcccattacag

Basic information

species Oryza sativa
transcript LOC_Os11g47330.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 4
GCACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaagatgcatatagaattcacttttcatttgttgtaatgttttagttgtaaatgtaa-taaacgtattggtctatcatgtatccataacaatatgctcccattacag
||||| |||||||||||||| |||||||||||||| ||||| || |||| |||||    ||||      |   || | ||  ||  ||| || |  |   | |||   ||||   || |  |  ||   |  |||||    | |  ||||||||||   | |||
GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAGgtaccgcagatttgggaattttttatttgccagctgtagtgaattaagaattgctcatgtcgctatatctcctgagttgccatgttgata-agaaatatgctccatctccag
















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|88690145|gb|CI734224.1|CI734224
EST:     ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAG                         ACTTAGATTTCTCATTTCTCGAGATG
genomic: ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaaga ... cccattacagACTTAGATTTCTCATTTCTCGAGATG
EST: gi|38478269|gb|CF962402.1|CF962402
EST:     ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAG                         ACTTAGATTTCTCATTT
genomic: ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaaga ... cccattacagACTTAGATTTCTCATTT
EST: gi|117247393|gb|CT848567.1|CT848567
EST:     ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAG                         ACTTAGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAG
genomic: ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaaga ... cccattacagACTTAGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAG
EST: gi|88690955|gb|CI735034.1|CI735034
EST:     ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAG                         ACTTAGATTTCTCATTTCTCGAGATGAACCCATTTAC
genomic: ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaaga ... cccattacagACTTAGATTTCTCATTTCTCGAGATGAACCCATTTAC
EST: gi|88690505|gb|CI734584.1|CI734584
EST:     ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAG                         ACTTAGATTTCTCATTTCTCGAGATGAACCCATT
genomic: ACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaaga ... cccattacagACTTAGATTTCTCATTTCTCGAGATGAACCCATT

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: 47 (upstream exon), 75 (downstream exon)
Score: 37

GCACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaaga ... cccattacagACTTAGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAGgtattaaagatgcatatagaattcacttttcatttgttgtaatgttttagttgtaaatgtaataaacgtattggtctatcatgtatccataacaatatgctcccattacag

- - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - -  GCTGTT