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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagagcgcaatttttgagatatctaagctgatgtctcgaatagttcagaacagtcagtcggaaccgcaagagccatcttcaccttaatctaatccttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTAGGTTTTCTAATGCAGCTTGCAAGATTCAGGGTTTGTATGGATTCATTTA

Basic information

species Oryza sativa
transcript LOC_Os06g50050.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50050.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G075584_T01 (Zea mays), 3'ss of exon 1
gtacagagcgcaatttttgagatatctaagctgatgtctcgaatagttcagaacagtcagtcggaaccgcaagagccatcttcaccttaatctaatccttttgctagATCTCATGAAAATCC---AAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTAGGTTTTCTAATGCAGCTTGCA---AGATTCAGGGTTTGTATGGATTCATTTA
||||||| ||| ||  |||||||||||||||||||||||||||||||| ||| ||| ||||| ||||| |||||||| |||||||||||||||||||||||||||||||| | ||||||| |   |  ||||||| |||||||||||| |||||| | ||||||||||| | ||||||||||   || ||||| || | |||  ||       
gtacagaacgcgatccttgagatatctaagctgatgtctcgaatagttgagagcagccagtcagaaccccaagagccttcttcaccttaatctaatccttttgctagATCGCGTGAAAATTCTACAGCGGAGTAAACGCAGGCATTACGTCGATACCCTTAGGTTTTCTTACGCAGCTTGCAGAGAGGTTCAGCGTATATATATATA------
















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|87022119|gb|CI259191.1|CI259191
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
EST: gi|29621240|gb|CB626251.1|CB626251
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
EST: gi|109712956|gb|CI105564.1|CI105564
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
EST: gi|88522651|gb|CI449480.1|CI449480
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
EST: gi|88511314|gb|CI438820.1|CI438820
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
EST: gi|88535200|gb|CI463985.1|CI463985
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
EST: gi|88535761|gb|CI465467.1|CI465467
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
EST: gi|33657032|gb|CF279646.1|CF279646
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTA
EST: gi|218482446|gb|FG948949.1|FG948949
EST:     GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAG                         ATCTCATGAAAATC
genomic: GGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATC

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: 70 (upstream exon), 71 (downstream exon)
Score: 13

TTTATCAACGTCTAGAAAGGGGAAAAGGGCCGCGAATGGAACATCTACGGGGTTGCAGTCACCGGTGTGGATTCGGCCCTCTGATTCAGAAGACGATCAGgtacagagcg ... cttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTAGGTTTTCTAATGCAGCTTGCAAGATTCAGGGTTTGTATGGATTCATTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtcagtcggaaccgcaagagccatcttcaccttaatctaatccttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTAGGTTTTCTAATGCAGCTTGCAAGATTCAGGGTTTGTATGGATTCATTTA
                                     atctaat  putative branch site (score: 13)
                                           tccttttgct  CT-rich tract
                                  ttaatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagagcgcaatttttgagatatctaagctgatgtctcgaatagttcagaacagtcagtcggaaccgcaagagccatcttcaccttaatctaatccttttgctagATCTCATGAAAATCCAAAGGAGTAAGCGCAGGCATTACCTCGATATCGTTAGGTTTTCTAATGCAGCTTGCAAGATTCAGGGTTTGTATGGATTCATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA