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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcactattcaccaaatgatcatctatatccttatcattcatctagcaacaatatttatgtaatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT

Basic information

species Oryza sativa
transcript LOC_Os11g04980.1
intron # 6
splice site 3'
intron type U2

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|29671403|gb|CB667678.1|CB667678
EST:     CGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: CGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|33676001|gb|CF304240.1|CF304240
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58696224|gb|CK084911.1|CK084911
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58690407|gb|CK079094.1|CK079094
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58611948|gb|CK039660.1|CK039660
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|33675052|gb|CF303291.1|CF303291
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58692164|gb|CK080851.1|CK080851
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGGGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58663800|gb|CK052486.1|CK052486
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT

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), 68 (downstream exon)
Score: 14

TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatcatctatatccttatcattcatctagcaacaatatttatgtaatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT
                                aacaatatttatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcactattcaccaaatgatcatctatatccttatcattcatctagcaacaatatttatgtaatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC