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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgactttgctacttgcttttatatgacaagaacaaatgccctattccatcgttttctttcttctaaaccttgtgttctttttcatattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG

Basic information

species Oryza sativa
transcript LOC_Os01g32800.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G868757_T02 (Zea mays), 3'ss of exon 1
gtatgactttgctacttgcttttatatgacaagaacaaatgccctattccatcgtt-ttctttcttctaaaccttgtgttctttttcatattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG
               |  | ||| |       |||    |  |  || ||| |    || | | ||    || |  |  |    ||||| ||  || |||||||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||| ||||||| ||||||||||||||||||||||
--------------gtaacctttgtg------gaatctttttctaatgccacctccattttctttttctgacatgttacttgccttcat-tttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG

upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 5
gtatgactt-tgctacttgcttttatatgacaagaacaaatgccctattccatcgttttctttcttctaaaccttgtgttctttttcatattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG
|||  | || ||  |  | ||||| ||            ||| |     ||  | |||||||| |  |  || |  | ||  | || || ||  || |||||||| ||||| |||||||| |||||||||||||| |||||||  ||||||||||| |||||||||||||| ||||| ||||||||||||||||||
gtaacatttgtggaatcttcttttcta------------atgtca----cctccattttctttttctttgacatgttatttgtctttat-tttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG
















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|56157812|gb|C26812.2|C26812
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|33806787|gb|CF329275.1|CF329275
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|87026926|gb|CI259579.1|CI259579
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|86854504|gb|CI256626.1|CI256626
EST:     TGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: TGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|27578052|gb|CB000747.1|CB000747
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|3759667|gb|C96925.1|C96925
EST:     AACTGCTAGAGAAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AACTGCTAGAG-AAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|14981128|gb|BI305819.1|BI305819
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|163925513|gb|EG715382.1|EG715382
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|163927856|gb|EG714236.1|EG714236
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
EST: gi|29687233|gb|CB683508.1|CB683508
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAC                         CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCAC

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: 73 (upstream exon), 67 (downstream exon)
Score: 14

TCCACAACGCTGCTCTTAGTGCACAGCCAGCTTTGGTGCAGAATGAACGAAAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTACgtatgacttt ... catattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctattccatcgttttctttcttctaaaccttgtgttctttttcatattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG
                       ttctaaa  putative branch site (score: 14)
                              ccttgtgttctttttc  CT-rich tract
                                     ttctttttcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgactttgctacttgcttttatatgacaagaacaaatgccctattccatcgttttctttcttctaaaccttgtgttctttttcatattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA