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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagacagtactggttcttgtgctgtcaatttcgggacttcagttttattaattattaacctgtgacatcaattttattctgactggtttctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCTCTAAATAAAGCAAGGAGCCTTATCCATCCACCTGTGAAGAAGCCATCCA

Basic information

species Oryza sativa
transcript LOC_Os01g03070.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03070.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G093050_T02 (Zea mays), 3'ss of exon 8
tcagacag--tactggttcttgtgctgtcaatttcgggacttcagttttattaattattaacctgtgacatcaattttattctgactggtttctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCTCTAAATAAAGCAAGGAGCCTTATCCATCCACCTGTGAAGAAGCCATCCA
| |    |  | ||| |   |||  | |   | | | |      |  ||| |   |  | |  |   |||  |||   ||| || ||| || || ||| |||||||| ||||||||| |  | ||| ||||||| |||||| | ||||||||  |||||||||||||||  | ||||  |||||| ||||| |||||||| |
ttaattggattgctgatatctgtcatatttttatggtgctggatgcattacttcatgatgagattgaacactaat--gattatgcctgattcctctttatagGACATAGAATCTGATGGCTTAAGTGATCACCTTAGTGTTCTTGCTGATTCATTAAATAAAGCAAGGATTCATATCTGTCCACCAGTGAAAAAGCCATCTA
















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|86427691|gb|CI072788.1|CI072788
EST:     TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATG                         GACATTGAATCTGATTGTCCCAGTAATCACCTAAGTGTTTTGGCTGATTCT
genomic: TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
EST: gi|89192877|gb|CI050175.1|CI050175
EST:     TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATG                         GACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
genomic: TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
EST: gi|88964806|gb|CI084804.1|CI084804
EST:     TTGCTATGAAAGACAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATG                         GACATTGAATCTGATTGTCTCAGTAACCACCTAAGTGTTTTGGCTGATTCT
genomic: TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
EST: gi|86429925|gb|CI082348.1|CI082348
EST:     TTGCTATGAAAGACAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATG                         GACATTGAATCTGATTGTCTCAGTAACCACCTAAGTGTTTTGGCTGATTCT
genomic: TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
EST: gi|89185749|gb|CI047618.1|CI047618
EST:     TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATG                         GACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
genomic: TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
EST: gi|88263846|gb|CI367620.1|CI367620
EST:     TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATG                         GACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
genomic: TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
EST: gi|58695557|gb|CK084244.1|CK084244
EST:     TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATG                         GACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
genomic: TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
EST: gi|86432397|gb|CI086008.1|CI086008
EST:     TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATG                         GACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT
genomic: TTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCT

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: 69 (upstream exon), 30 (downstream exon)
Score: 51

CTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGAAACACAATTTTGTTGCTATGAAAGTCAACCATTTATCAGGAGCTGTCCATTTTGGGAAAATGgtatgtggtt ... ctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCTCTAAATAAAGCAAGGAGCCTTATCCATCCACCTGTGAAGAAGCCATCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattaattattaacctgtgacatcaattttattctgactggtttctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCTCTAAATAAAGCAAGGAGCCTTATCCATCCACCTGTGAAGAAGCCATCCA
                                          tttctgttt  CT-rich tract
                    acatcaattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagacagtactggttcttgtgctgtcaatttcgggacttcagttttattaattattaacctgtgacatcaattttattctgactggtttctgtttgtagGACATTGAATCTGATTGTCTCAGTAATCACCTAAGTGTTTTGGCTGATTCTCTAAATAAAGCAAGGAGCCTTATCCATCCACCTGTGAAGAAGCCATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - ctggttc
- - - - - - - - - - tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtgac