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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgcagtgttgctataagggaaatacttgttgtattttatttgtgcacataaaaccatgaaattgttgtaatcaagcatttcttttgaatcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTGTTCGTGGTGGTCGTTGCTCTTCTGGGAATTCTACTGGGGTATATCATGA

Basic information

species Oryza sativa
transcript LOC_Os04g45190.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G155543_T01 (Zea mays), 3'ss of exon 8
ttatgcagtgttgctataagggaaatacttgttgtattttatttg---tgcacataaaaccatgaaattgttgtaatcaagcatttcttttgaatcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTGTTCGTGGTGGTCGTTGCTCTTCTGGGAATTCTACTGGGGTATATCATGA
  ||| | |  |  |   |      ||  ||   |   | | | |   ||||  || ||  ||   |   ||||||  ||  | |  |  ||||||  || ||||||||  ||||||||||   | ||||||||||||||| ||| | |||||| ||||||||| | ||||||| |||||||| |||||||| ||||||||||
--atgaatttctagt-cgaactttttatatggcatccataactagctctgcatgtagaaatattgtacatttgtaactaaaaagtcttgctgaatcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA
















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|88691550|gb|CI733628.1|CI733628
EST:     AAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATG                         GACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
genomic: AAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
EST: gi|88520888|gb|CI448542.1|CI448542
EST:     AAGAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATG                         GACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
genomic: AAGAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
EST: gi|88688963|gb|CI732539.1|CI732539
EST:     AAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATG                         GACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
genomic: AAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
EST: gi|86893296|gb|CI313417.1|CI313417
EST:     GAAAGAAACTCTCCTATTCAGCAGAACAATAATCTTCTCGAGGAGATG                         GACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
genomic: GAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
EST: gi|27547307|gb|CA765509.2|CA765509
EST:     AAGAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATG                         GACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
genomic: AAGAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
EST: gi|25803588|gb|CA759549.1|CA759549
EST:     AAGAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATG                         GACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
genomic: AAGAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG
EST: gi|86600861|gb|CI356618.1|CI356618
EST:     CTCGAGGAGATG                         GACCTTGTGAGGAGGGAAATTAGCAAGCAAGAATGGTGGTTTCCACTTTTG
genomic: CTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGC-AGAATGGTGGTTTCC-CTTTTG
EST: gi|88470081|gb|CI407352.1|CI407352
EST:     GAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATG                         GACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTT
genomic: GAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTG

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: 58 (upstream exon), 44 (downstream exon)
Score: 4

ACATCTGCTTTGATTTCAAGATTGACAGAAGAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATGgttagtagat ... atcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTGTTCGTGGTGGTCGTTGCTCTTCTGGGAATTCTACTGGGGTATATCATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacataaaaccatgaaattgttgtaatcaagcatttcttttgaatcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTGTTCGTGGTGGTCGTTGCTCTTCTGGGAATTCTACTGGGGTATATCATGA
                                  atttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgcagtgttgctataagggaaatacttgttgtattttatttgtgcacataaaaccatgaaattgttgtaatcaagcatttcttttgaatcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTGTTCGTGGTGGTCGTTGCTCTTCTGGGAATTCTACTGGGGTATATCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
ttatgca
- - - - tgttgct
- - - - - - - - -aagggaaa
- - - - - - - - - - - - - -cttgttg
- - - - - - - - - - - - - - ttgttgt
- - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - -cataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgaa