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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTCAATCTCAGTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtcgtttttgcctgatcgaaaactgcatttttttttgtgactctgagactaattctttgttaactcattgacag

Basic information

species Oryza sativa
transcript LOC_Os06g49990.1
intron # 14
splice site 5'
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|88566864|gb|CI497581.1|CI497581
EST:     CTGCATTAATGGTTAGACAGTGCTGGTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88419114|gb|CI511266.1|CI511266
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88461847|gb|CI506923.1|CI506923
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTGTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88428127|gb|CI557021.1|CI557021
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88565703|gb|CI496420.1|CI496420
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTTTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88292813|gb|CI505392.1|CI505392
EST:     CTGCATTGATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAGG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88564335|gb|CI495052.1|CI495052
EST:     CTGCATTAATGGTTAGACAGTGCTGGTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGC
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCT-GGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGC
EST: gi|88469090|gb|CI504810.1|CI504810
EST:     TGCATTAATAGTTAAACAGTGCTGCTACTCCAAATGGGACTCTAGGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCGGCGCTCAGCATGGATAAGC
genomic: TGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTA-GAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGC
EST: gi|88367970|gb|CI561558.1|CI561558
EST:     CTGCATTAATGGTTAGACAGTGCTGGTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88418808|gb|CI506569.1|CI506569
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88384956|gb|CI559224.1|CI559224
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88292382|gb|CI500330.1|CI500330
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88432142|gb|CI562973.1|CI562973
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|88565726|gb|CI496443.1|CI496443
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
EST: gi|313080000|gb|HO213320.1|HO213320
EST:     CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG                         TGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA
genomic: CTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCA

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: 36 (upstream exon), 53 (downstream exon)
Score: 4

AATTTCAATCTCAGTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtc ... tcattgacagTGCTTGGTTCTGGCCATGGAATGCAGCCGCAGCGCTCAGCATGGATAAGCATCACTACCTTGTATTCATTCTGTAGATACAACTCATTGTACAGGAACTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTTCAATCTCAGTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAGgtatttagtcgtttttgcctgatcgaaaactgcatttttttttgtgactctgagactaattctttgttaactcattgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT