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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttggctcctggattatctgatatatctgaatgaataccaacacgatcaattccaaggtatcttcttgtgtgcttataagtacagttttgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATATTAGGCAACACTACTGAAGAATTGGTGATGCGAGCGCAACAGAGCCCAA

Basic information

species Oryza sativa
transcript LOC_Os12g29550.1
intron # 14
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|88543538|gb|CI473556.1|CI473556
EST:     TTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: TTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|89177578|gb|CI390757.1|CI390757
EST:     CTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: CTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|86884897|gb|CI314473.1|CI314473
EST:     ATGTTCGTGATGCT-TAAAGAAATTGGAGAGGCTT-GTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88976163|gb|CI024384.1|CI024384
EST:     GATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: GATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88200109|gb|CI199959.1|CI199959
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88537782|gb|CI466757.1|CI466757
EST:     AGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: AGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88381075|gb|CI523646.1|CI523646
EST:     CTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: CTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|86873701|gb|CI341134.1|CI341134
EST:     GGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: GGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|27920788|gb|CB096596.1|CB096596
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|89177439|gb|CI390618.1|CI390618
EST:     ATGTTCGTGATGCT-TAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|29646633|gb|CB651640.1|CB651640
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|163928795|gb|EG709723.1|EG709723
EST:     TGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: TGTTCGTGATGCTGTAAAGAAATTGGAGAGGC-TTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88321239|gb|CI532989.1|CI532989
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|86417794|gb|CI032003.1|CI032003
EST:     CGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: CGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|29666115|gb|CB662390.1|CB662390
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|87012979|gb|CI297206.1|CI297206
EST:     GATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: GATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|86871032|gb|CI328234.1|CI328234
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|58595569|gb|CK006097.1|CK006097
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCCATTGGAAGGATTGTCTGTGTCTCATT
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATT
EST: gi|88469418|gb|CI406689.1|CI406689
EST:     AGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: AGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88455822|gb|CI524241.1|CI524241
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88282536|gb|CI403932.1|CI403932
EST:     CTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTTTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: CTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88283924|gb|CI405370.1|CI405370
EST:     CTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: CTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88281736|gb|CI403132.1|CI403132
EST:     GAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: GAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|86869535|gb|CI346395.1|CI346395
EST:     ATGTTCGTGATCCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
EST: gi|88486405|gb|CI423676.1|CI423676
EST:     ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGG                         GACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA
genomic: ATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATA

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), 73 (downstream exon)
Score: 21

GCGCTGTGAAGAGCTAATTAAGGAAGAGTTTGGTGCAGAGTGCAATTTTGATGTTCGTGATGCTGTAAAGAAATTGGAGAGGCTTGGTATCGTTCATCGGgtaaatctct ... tgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATATTAGGCAACACTACTGAAGAATTGGTGATGCGAGCGCAACAGAGCCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatcaattccaaggtatcttcttgtgtgcttataagtacagttttgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATATTAGGCAACACTACTGAAGAATTGGTGATGCGAGCGCAACAGAGCCCAA
                                          ttttgct  CT-rich tract
                              ttataagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttggctcctggattatctgatatatctgaatgaataccaacacgatcaattccaaggtatcttcttgtgtgcttataagtacagttttgctgctcagGACTCGATTGGAAGGATTGTCTGTGTCTCATTGAAGCGTGCAAATGAGATATTAGGCAACACTACTGAAGAATTGGTGATGCGAGCGCAACAGAGCCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - gctcctg
- - - - - - - - - - - - - - ctgaatg
- - - - - - - - - - - - - - - - - - ataccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttat