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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctgcctctctgcctctgttaatttcttctctcggtcctcttgatactgtagtactatgcagtgggtaattaacagagcatgtatacaaataatctaaatataaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCACTGGTGGAGCACCTCAAGGCCAACCCCATGTTCCGCGTCGGTCTTGATG

Basic information

species Oryza sativa
transcript LOC_Os02g01150.2
intron # 8
splice site 3'
intron type U2

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|38477990|gb|CF962123.1|CF962123
EST:     AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG                         GAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
genomic: AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
EST: gi|10794734|gb|AU108700.1|AU108700
EST:     GACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCCATCATGAAGAAG                         GAAGCGGNTCTTGTGAATGCAAGTCGAGGACCGGTGATT
genomic: GACCACTTACCATCTGATAAACCCGGAAAGGCTGGCC-ATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATT
EST: gi|29682997|gb|CB679272.1|CB679272
EST:     AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG                         GAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGAGATTGATGAGGTATCA
genomic: AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
EST: gi|117233241|gb|CT848054.1|CT848054
EST:     AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG                         GAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
genomic: AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
EST: gi|11442863|gb|BF430762.1|BF430762
EST:     AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG                         GAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
genomic: AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
EST: gi|86906454|gb|CI294577.1|CI294577
EST:     AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG                         GAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
genomic: AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
EST: gi|58605093|gb|CK033126.1|CK033126
EST:     AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG                         GAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGGG
genomic: AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
EST: gi|58593170|gb|CF991478.1|CF991478
EST:     GGAAAGGCTGGCCATCATGAAGAAG                         GAAGCGGTTCTTGTGAATGCAAGTCGAGGAGCGGTGATTGATGAGGTAGCA
genomic: GGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
EST: gi|38481826|gb|CF965897.1|CF965897
EST:     AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG                         GAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA
genomic: AGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCA

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: 69 (upstream exon), 71 (downstream exon)
Score: 43

ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAGgtgcctgcct ... aaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCACTGGTGGAGCACCTCAAGGCCAACCCCATGTTCCGCGTCGGTCTTGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagtgggtaattaacagagcatgtatacaaataatctaaatataaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCACTGGTGGAGCACCTCAAGGCCAACCCCATGTTCCGCGTCGGTCTTGATG
                      atgtatacaaataatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctgcctctctgcctctgttaatttcttctctcggtcctcttgatactgtagtactatgcagtgggtaattaacagagcatgtatacaaataatctaaatataaaaatacagGAAGCGGTTCTTGTGAATGCAAGTCGAGGACCGGTGATTGATGAGGTAGCACTGGTGGAGCACCTCAAGGCCAACCCCATGTTCCGCGTCGGTCTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA