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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGTCGTACTCTTTGTCTGCAGCCGGCGAGCAGATCTGAAGGCGCGGCCGGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgattacttccctcgcgtagattgcaaattcatcagggctttgattgattggtctccgtccaatcaaaccgtcgagtttgttgtgaatttattt...

Basic information

species Oryza sativa
transcript LOC_Os05g36070.2
intron # 1
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|88430529|gb|CI569552.1|CI569552
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|29625862|gb|CB630873.1|CB630873
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|29623040|gb|CB628051.1|CB628051
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|58656513|gb|CK045193.1|CK045193
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|88725058|gb|CI748317.1|CI748317
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|29623038|gb|CB628049.1|CB628049
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|319908628|gb|HS977756.1|HS977756
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|88395446|gb|CI612968.1|CI612968
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|58662178|gb|CK050858.1|CK050858
EST:     GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGGAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
EST: gi|88395445|gb|CI612967.1|CI612967
EST:     GGCCGACCTCCTCCCGCCTACCTCAACTCTCGTCTCGACTCGAATTGAAG                         AAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA
genomic: GGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGA

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: 68 (upstream exon), 74 (downstream exon)
Score: 13

CCGGTCGTACTCTTTGTCTGCAGCCGGCGAGCAGATCTGAAGGCGCGGCCGGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgat ... tatatctcagAAGGGACAATACCGTGAAGTATCTGGGCTGTTGCTTCGTTATTTTCGTGGATTCACCTTGGAACTTCAGAACGAATCTTCCTGATATTTTCCGTGACAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGTCGTACTCTTTGTCTGCAGCCGGCGAGCAGATCTGAAGGCGCGGCCGGCCGACCTCCTCCCGCCTACCTCAAGTCTCGTCTCGACTCGAATTGAAGgtcttgcgattacttccctcgcgtagattgcaaattcatcagggctttgattgattggtctccgtccaatcaaaccgtcgagtttgttgtgaatttattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccgtcc