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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGTGGGGAACAAATAGACCTTTCTGGTACAGGCTCATTTTATAATGATGGAGAGGCAGATATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacatttttttttagactggtggtatgtacatatttctactttaattagatattgccttggacattgttttaccaatttaaggctctttttgtat...

Basic information

species Oryza sativa
transcript LOC_Os02g47560.1
intron # 2
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|88669550|gb|CI723214.1|CI723214
EST:     ATTGTAACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88676395|gb|CI730508.1|CI730508
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88665622|gb|CI715778.1|CI715778
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|89172152|gb|CI721211.1|CI721211
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88668007|gb|CI722746.1|CI722746
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88669799|gb|CI723915.1|CI723915
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88671306|gb|CI724352.1|CI724352
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88671068|gb|CI725184.1|CI725184
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88668823|gb|CI719780.1|CI719780
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88676987|gb|CI731100.1|CI731100
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88593507|gb|CI713461.1|CI713461
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88677056|gb|CI731169.1|CI731169
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88671100|gb|CI725216.1|CI725216
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88671307|gb|CI724353.1|CI724353
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88665896|gb|CI716052.1|CI716052
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88677001|gb|CI731114.1|CI731114
EST:     ATTGTAACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88671823|gb|CI725358.1|CI725358
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88908969|gb|CI716693.1|CI716693
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88674583|gb|CI728696.1|CI728696
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88675511|gb|CI729624.1|CI729624
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88671692|gb|CI725723.1|CI725723
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88594617|gb|CI714575.1|CI714575
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88666399|gb|CI716555.1|CI716555
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88669680|gb|CI723796.1|CI723796
EST:     ATTGTAACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88671687|gb|CI725718.1|CI725718
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88670865|gb|CI724981.1|CI724981
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
EST: gi|88669895|gb|CI724011.1|CI724011
EST:     ATTGTGACACAACATGTTCTCAACCTTGTACATTGTG                         GAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC
genomic: ATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGC

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: 72 (upstream exon), 73 (downstream exon)
Score: 31

GGTTGTGGGGAACAAATAGACCTTTCTGGTACAGGCTCATTTTATAATGATGGAGAGGCAGATATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacat ... atgatcgcagGAGTATCTCCAACAGCGATAGCCGTTCAATCACCCTACATTGCTCAAGTGCAGTTGTTAAGAGAGAGGCTAGAAGAATATCCAGGGCTTTCTGGGGTTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGTGGGGAACAAATAGACCTTTCTGGTACAGGCTCATTTTATAATGATGGAGAGGCAGATATTGTGACACAACATGTTCTCAACCTTGTACATTGTGgtatgtacatttttttttagactggtggtatgtacatatttctactttaattagatattgccttggacattgttttaccaatttaaggctctttttgtat

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT