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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgatcaagctgatgccatcatggaaatggttgcatattagcattgataaaatatttgctctacttgctagttgagcctttaattttctcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGCTGAGGCCAATGGAGGGTACAATCTGCAG

Basic information

species Oryza sativa
transcript LOC_Os10g34400.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g34400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G079428_T01 (Zea mays), 3'ss of exon 4
cattgatcaagctgatgccatcatgg--aaatggttgcatattagcattgataaaatatttgctctacttgctagttgagcctttaattttctct-tgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGCTGAGGCCAATGGAGGGTACAATCTGCAG
  ||     |  | ||   |  |  |  |||||  |  |  |||   |  || ||||||||| | | | ||||   |||    |||||| |||   | ||||| ||||||  ||| ||  |||||||| |||| ||||||||||| |||||||| ||||| ||||| || || || || |||
tcttagctgatttcattttactagtgtaaaatgtctttactttattgt--atgaaatatttg-tttgcatgctgaatgacttcttaattctcttcattttcagACAGCTGGCTTCTGACAGCCCTGGTCTCCCTATATTTGAAATATACTTTGCAGAGGCAAATGGTGGATATAACCTACAG

upper sequence: LOC_Os10g34400.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G048435_T01 (Zea mays), 3'ss of exon 4
cattgatcaagctgatgccatcatggaaa---tggttgcatatt--agcattgataaaatatttgctctacttgctagttgagcctttaattttc-tcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGCTGAGGCCAATGGAGGGTACAATCTGCAG
      ||    | |||  || ||  | |       ||| ||||  || |   |  ||||||||| | | | |||||  |||   ||||||| || || | ||||| ||||||| ||| ||  || ||||| |||| ||||||||||| |||||||| ||||| ||||| || ||||| ||||||
-----ttcttattcatgtaattatacacaactctcctgcgtattcgagaaaaaaagaaatatttg-tttgcatgctaaatgactttttaattctcctcattttcagACAGCTGACTTCTGACAGCTCTGGTCTCCCTATATTTGAAATATACTTTGCAGAGGCAAATGGTGGATACAACCTGCAG
















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|58694399|gb|CK083086.1|CK083086
EST:     CGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAG                         GCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGC
genomic: CGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAGgtaatagttg ... tcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGC
EST: gi|29628475|gb|CB633486.1|CB633486
EST:     CGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAG                         GCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGC
genomic: CGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAGgtaatagttg ... tcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGC
EST: gi|56157749|gb|C26223.2|C26223
EST:     CGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAG                         GCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGC
genomic: CGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAGgtaatagttg ... tcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGC
EST: gi|66926056|gb|CX112904.1|CX112904
EST:     CGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAG                         GCAGCTGAATTCAGATGGCCCTGGTTTCCCCA
genomic: CGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAGgtaatagttg ... tcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCA

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: 75 (upstream exon), 73 (downstream exon)
Score: 21

GGTGGTCTGGGATTTCTGGAAATTTGTCTGATCCATATGGTCTTATAATTCGTATAAGTGCTGAACATGGTCGATATGTGGCGAAAAGTTACGATACCAGgtaatagttg ... tcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGCTGAGGCCAATGGAGGGTACAATCTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgataaaatatttgctctacttgctagttgagcctttaattttctcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGCTGAGGCCAATGGAGGGTACAATCTGCAG
                                  ctttaat  putative branch site (score: 21)
                                 cctttaattttctctt  CT-rich tract
                                   tttaattttctctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgatcaagctgatgccatcatggaaatggttgcatattagcattgataaaatatttgctctacttgctagttgagcctttaattttctcttgttcagGCAGCTGAATTCAGATGGCCCTGGTTTCCCCATATTTGAAATTTACTTTGCTGAGGCCAATGGAGGGTACAATCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - tgatgcc
- - - - - - - - - - -catggaa
- - - - - - - - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgcta