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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaacatgtaagcgctgttattctagcattattgaataatttttatgcataatttaatccctttactcttattcctgaatccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT

Basic information

species Oryza sativa
transcript LOC_Os03g63520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 2
agaacatgtaagcgctgttattctagcattattgaataatttttatgcataatttaatccctttactcttattcctgaatccatct---tttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
    |     ||   | | |||         ||| ||  | |||||    |  | ||   ||| || |||||     || |   ||   ||| || |||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||| |||||||||||||| |||||||| ||||||||
---tcgctccagacttataattactattaggttgcatgctgtttatttgcatctcaagtgcttcacccttataataaaaacttactctctttcttttttccagATTTGGATTTTCTGTTCCACATGTTTTTTCTCGCACGATACTGCAAGCTTCTGGAGGAGAACTCATTTAGAGGAAGAACTGCCGACTTTTTTTACATGCT

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G112609_T01 (Zea mays), 3'ss of exon 2
agaacatgtaagcgctgttatt-ctagcattattgaataatttttatgcataatttaatccctttactcttattcctgaatccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
  | |||   ||   | | ||| ||   |  ||||  || | |||||    | || ||   ||| || |||||   ||||  | |  | | ||    ||||||||||| ||||| ||||||||||| ||||||||||| |||||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||
gcatcattccagacttataattactgttagcattgcttactgtttatttgcatttcaagtgcttcacccttataa-tgaagacctactctttttcccccagATTTGGATTTTCTATTCCACATGTTCTTTCTTGCACGGTACTGCAAGCTTCTGGAGGAAAACTCATTTAGAGGAAGAACTGCTGACTTTTTTTACATGCT

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 2
-agaacatgtaagcgctgttattctagcattattgaataatttttatgcataatttaatccctttactcttattcctgaatccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
 | |||   ||  |    || ||  |  ||  ||  ||| ||  |  | |   | |    | | ||   ||      | ||   |||| |    |   |||| ||||| || ||||| || |||||||||||||| || |||||||||||||||||||||||||| ||||| || || |||||||| || || ||||||||
aataacccttattcttatttgtttcataatcgtttgatatttaattagaaagttatgcatcttctaaatttgacatggtattt-tcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCTCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G11350.2 (Glycine max), 3'ss of exon 2
agaacatgtaagcgctgtt-attctagcattattgaataatttttatgcataatttaatccctttactcttattcctgaatccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
| |   | |  || || ||  ||  | |||  ||  ||  ||  |  | | | | |    | | ||   ||      | ||   |||| |    |   |||| ||||| || ||||| || |||||||||||||| || |||||||||||||||||||||||||| ||||| || || |||||||| || || ||||||||
atattctctttgctctctttgtttcatcatcgtttgatgtttaattagaaaattgtgcatcttctaaatttgacatggtattt-tcttattgaatgggcagACTTGGATTTCCTGTTTCATATGTTTTTTCTTGCCCGTTACTGCAAGCTTCTTGAGGAGAACTCGTTCAGGGGGAGGACTGCTGATTTCTTTTACATGCT

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G21810.1 (Arabidopsis thaliana), 3'ss of exon 2
------agaacatgta-agcgctgttattctagcattattgaataatttttatgcataatttaatccctttactcttattcctga-atccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
         |||| |  ||  || |  | |  | |    |  ||  | ||| || ||  || | |         ||| ||| ||  ||| ||||||||       |||||||||||||| ||||||| ||||||||||| || ||||||||||| || || || || ||||| ||||| ||||  || || || ||  | ||||||||
tgctccttgacatctctagtactatgctccctgtaaggatttattttctttgtg-attgttaattagaagctgacttgttcttgttatcaatcttttg-------cagATTTGGACTTTTTGTTCCATATGTTTTTTCTAGCTCGATACTGCAAACTGCTCGAAGAAAACTCCTTCAGGGGAAAGACCGCGGATTTCCTTTACATGCT

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------agaacatgtaagcgctgttattctagcattatt-------gaataatttttatgcataa---tttaatccctttact-cttattcctgaatccatcttttgttgt-ttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
                                                              | ||| |     |||  || |  |||||||       |  |  |  || |  |||    | | |    || | | |||||     |||   | ||| |   | ||  ||||||||||||  ||||||| ||||| ||||| |||||||||||||| || ||||| || ||||||||||| ||||  |||||||| ||  | ||||||||
gtaattttcccttaacactactctatgaaactggatacaacatttgtgtgcttattactttcatatgaagctcttgtctttgtcacattattagctctaggctgctacttgttaatagcgttgtgactgattgattgcttataaacaaatatgtgtttggggttgttgtagATTTGGACTTCATGTTCCATATGTTCTTTCTCGCACGATACTGCAAACTCCTTGAAGAAAACTCATTCAGGGGAAAGACTGCTGATTTCCTATACATGCT

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|88348838|gb|CI631925.1|CI631925
EST:     TACGAGATCTGGCGCCTCGTCACCAACTTCCTCTAACTTC-GTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCANGATACTGCAAGCTTC
genomic: TACGAGATCTGGCGCCTCGTCACCAACTTCCTCTA-CTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
EST: gi|88717592|gb|CI741102.1|CI741102
EST:     CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTT
genomic: CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTT
EST: gi|117223453|gb|CT848631.1|CT848631
EST:     CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
genomic: CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
EST: gi|33683707|gb|CF311946.1|CF311946
EST:     CTACGAGATCTGGCGCCTCGTCGCCAACTTCCTCTACTTCCGTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
genomic: CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
EST: gi|87006538|gb|CI294921.1|CI294921
EST:     CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
genomic: CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
EST: gi|88403631|gb|CI575515.1|CI575515
EST:     CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
genomic: CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
EST: gi|88397381|gb|CI580891.1|CI580891
EST:     CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
genomic: CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
EST: gi|88398700|gb|CI598665.1|CI598665
EST:     CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
genomic: CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
EST: gi|88354906|gb|CI615787.1|CI615787
EST:     CTACGAGATCTGGCGCCTCGTCAC-AACTTCCTCTACTTCCGTAAGATGG                         ATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC
genomic: CTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTC

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: 54 (upstream exon), 70 (downstream exon)
Score: 32

ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCACTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGGgtatgcgcct ... ttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcataatttaatccctttactcttattcctgaatccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT
      atttaat  putative branch site (score: 32)
                                      tcttttgttgtttcc  putative PPT
     aatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaacatgtaagcgctgttattctagcattattgaataatttttatgcataatttaatccctttactcttattcctgaatccatcttttgttgtttccagATTTGGACTTTCTGTTCCACATGTTTTTTCTTGCACGATACTGCAAGCTTCTTGAGGAGAACTCATTCAGAGGAAGAACTGCTGACTTTTTCTACATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- aacatgt
- - - - - - cgctgtt
- - - - - - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttttg