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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcttgtatcttttcttattgcgatactggagtttgtatataggaccacacttgatttttccacataaaaagggaaatccatccttaacttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAGCTCTTGCCATCTGTTCCTGGCACAATGAATATCCCATATGATGTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os01g48270.1
intron # 9
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G115766_T02 (Zea mays), 3'ss of exon 8
attcttgtatcttttcttattgcgatactggagtttgtatataggaccacacttgatttttccacataaaaagggaaatccatcct--taacttg-caattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAGCTCTTGCCATCTGTTCCTGGCACAATGAATATCCCATATGATGTTCTTG
   |||    ||    |         |     |||| |  ||   | |  |     |  |  || ||   |||| |  |   |||   ||||||| |||| ||||||||||||| || |||||||  || ||||||||||| ||||||||||||||| |||||| |   |||||||||||| | || || |||||||||||||
--ccttaaccctcccttcgccaaaccatctctgttttttaatcaaagctgaaacc-tcatgacaaatctgaaggaacttttttccccataacttgtcaatcagATTCTTGTTCCATTGCCAGAGCCGGATGCTAGACATGCTATGTTTGAAGAGCTCCTGCCATATACACCTGGCACAATGGAGATTCCCTATGATGTTCTTG
















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|163918009|gb|EG715247.1|EG715247
EST:     ATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAACGT                         ATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG
genomic: ATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAACGTgtatcctttt ... ttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG
EST: gi|4714792|gb|AU055909.1|AU055909
EST:     CCGTTTGGAGAAACGT                         ATTC-TGGTCCCTTCCCAGAGCAAGAAGCTA-ACATGCCATGTTTGAAGAG
genomic: CCGTTTGGAGAAACGTgtatcctttt ... ttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG
EST: gi|11565056|gb|AU165692.1|AU165692
EST:     GTTGCNCCGTTTGGAAGAAACGT                         ATTCNTGGTCCCNTTACCAGAGCAAGAAAGCTAGACATGCCATGTTTGAA
genomic: GTTGCGCCGTTTGG-AGAAACGTgtatcctttt ... ttgcaattagATTCTTGTTCCC-TTACCAGAGCAAG-AAGCTAGACATGCCATGTTTGAA
EST: gi|117243388|gb|CT843439.1|CT843439
EST:     ATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAACGT                         ATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG
genomic: ATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAACGTgtatcctttt ... ttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG
EST: gi|86498107|gb|CI140740.1|CI140740
EST:     ATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAACGT                         ATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG
genomic: ATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAACGTgtatcctttt ... ttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG
EST: gi|2428954|gb|C73417.1|C73417
EST:     ATGCAGCAATGTTGCGCCGTTTGGAGAAACGT                         ATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG
genomic: ATGCAGCAATGTTGCGCCGTTTGGAGAAACGTgtatcctttt ... ttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAG

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: 47 (upstream exon), 40 (downstream exon)
Score: 7

GGATGGGTTAACTAAGACAGATGATCTCGTTTTTGTTCTAGCCGCCACAAATTTGCCATGGGAACTGGATGCAGCAATGTTGCGCCGTTTGGAGAAACGTgtatcctttt ... ttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAGCTCTTGCCATCTGTTCCTGGCACAATGAATATCCCATATGATGTTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accacacttgatttttccacataaaaagggaaatccatccttaacttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAGCTCTTGCCATCTGTTCCTGGCACAATGAATATCCCATATGATGTTCTTG
                                    atccttaac  putative branch site 
       ttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcttgtatcttttcttattgcgatactggagtttgtatataggaccacacttgatttttccacataaaaagggaaatccatccttaacttgcaattagATTCTTGTTCCCTTACCAGAGCAAGAAGCTAGACATGCCATGTTTGAAGAGCTCTTGCCATCTGTTCCTGGCACAATGAATATCCCATATGATGTTCTTG

attcttg
- - - - - - - - - - - -gatactg
- - - - - - - - - - - - - - - - - - - - - -ggaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccatcc