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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgcctctcgcaagcggccaagcgcgatagattggtatagacagataaatcctgcaactgcgatacgattccgtcaccgaatcccttgtttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGTGCGGCGCATTGAGCCCAGCGTGCGAGGGGGCATGGATCTGGAGGCCGCG

Basic information

species Oryza sativa
transcript LOC_Os02g49760.3
intron # 1
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|88367250|gb|CI564014.1|CI564014
EST:     CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
EST: gi|88762424|gb|CI771980.1|CI771980
EST:     CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
EST: gi|88327994|gb|CI648399.1|CI648399
EST:     CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
EST: gi|88307477|gb|CI643321.1|CI643321
EST:     CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
EST: gi|88423254|gb|CI576379.1|CI576379
EST:     CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
EST: gi|88424398|gb|CI607984.1|CI607984
EST:     AAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACCGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGG
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGA-CGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGG
EST: gi|88389072|gb|CI595306.1|CI595306
EST:     CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
EST: gi|88454228|gb|CI567833.1|CI567833
EST:     AAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
EST: gi|88312007|gb|CI580172.1|CI580172
EST:     CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTG                         CAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT
genomic: CAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGT

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: 43 (upstream exon), 50 (downstream exon)
Score: 3

ACCTTCGGCTGATACAAGAAGCGAGGGGGAGGTAGGAGAGAAGCCCACCACAGGGTGACCCCATCGGCCATCGCGACATCTTCTTCTTCTTGCTCGCTTGgttggttgct ... ttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGTGCGGCGCATTGAGCCCAGCGTGCGAGGGGGCATGGATCTGGAGGCCGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatcctgcaactgcgatacgattccgtcaccgaatcccttgtttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGTGCGGCGCATTGAGCCCAGCGTGCGAGGGGGCATGGATCTGGAGGCCGCG
                                     tcccttgtttccttgc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgcctctcgcaagcggccaagcgcgatagattggtatagacagataaatcctgcaactgcgatacgattccgtcaccgaatcccttgtttccttgcagCAATTTGACGCCGCGAGGGCGGGTGGTTTCGTGGCCATGGCGGTCTCCGGTGCGGCGCATTGAGCCCAGCGTGCGAGGGGGCATGGATCTGGAGGCCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
cctgcct
- - - - -cgcaagc
- - - - - - - - -gccaagc
- - - - - - - - - - - - - - - - - - - - - cagataaa
- - - - - - - - - - - - - - - - - - - - - - - - - tcctgca