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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttaagctacctagatgttgacaaagtgtatgaaggaccgcagcacattttcttgtgttctgtttgattgatcatatggtgtgatactgctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g38620.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081924_T01 (Zea mays), 3'ss of exon 5
ctttaagctacctagatgttgacaaagtgtatgaaggaccgcagcacattttcttgtgtt-ctgtttgattgatcatatggtgtgatactg--------ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
         |      | |||    | | | ||  | |  |||   | |  | |  | ||  ||||||||||  |||||||||||||| ||        |||| |||||| ||  |||||||||||||||||||||| |||| |||||||||||||
---------attctcgttttggtgtattatgtggtgcattgcattccttactatgtttttattgtttgattgtccatatggtgtgataatgtggtaatgctttatgtagGCATACCATATCCTGAAAAGGAAGAAGTTCGTATCCTTCTAAGGCAG

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G142984_T01 (Zea mays), 3'ss of exon 5
ctttaagctacctagatgttgacaaagtgtatgaaggaccgcagcacattttcttgtgttctgtttgattgatcatatggtgtgatactg--------ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
       |    | ||   |      ||| ||      || || ||   | | || | |  ||||||||||  |||||||||||||||||        |||| |||||| ||   ||||||||||||||||||||||||||||||||||||||||
-------cgttttggagaattgtgtggtgcattgcattcctcatcattgtatgtt-tttattgtttgattgtacatatggtgtgatactgtggtactgctttatgtagGCATACTATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
















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|27577389|gb|CB000084.1|CB000084
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|33795398|gb|CF323569.1|CF323569
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|38472674|gb|CF956806.1|CF956806
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|86908033|gb|CI298799.1|CI298799
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|218495275|gb|FG966279.1|FG966279
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|218500721|gb|FG955417.1|FG955417
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|33793613|gb|CF322690.1|CF322690
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|38478638|gb|CF962771.1|CF962771
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGA
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGA
EST: gi|58655403|gb|CK044083.1|CK044083
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|27577933|gb|CB000628.1|CB000628
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
EST: gi|25801465|gb|CA757426.1|CA757426
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGA
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGA
EST: gi|218499923|gb|FG954899.1|FG954899
EST:     CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTG                         GAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
genomic: CGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG

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), 47 (downstream exon)
Score: 704

ATCGCTTATTCTCTGTTAGAGGAGCAGGAAGGGAAAAAGAGAGGATACGATGAGTACATATCTTTTGTCAGCCTCCTTGCTGATCCCCGATATTGTGgtacttacta ... ctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattttcttgtgttctgtttgattgatcatatggtgtgatactgctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG
                     gattgat  putative branch site (score: 704)
                                          ctgcttt  putative PPT
                  tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttaagctacctagatgttgacaaagtgtatgaaggaccgcagcacattttcttgtgttctgtttgattgatcatatggtgtgatactgctttgtgtagGAATGGCATATCCTGAAAAGGAAGAAGTCCGTACCCTTCTAAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT