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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaacatctctagcctatgtctattgccacctttttggaccatgtagcaaatctaaaatccaaatttcatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCCACAGAGCTTGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT

Basic information

species Oryza sativa
transcript LOC_Os11g01439.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------gttaacatctctag---cctatgtctattgccacctttttggaccatgta-gcaaatctaaaatccaaatttcatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCCACAGAGCTTGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT---------------------
                                                     ||| | ||    | ||||    | |  |   ||||   |   ||| |||  |  |  | |  |||    | ||   |||||||  ||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||  |||| |||||||| ||| ||||||| |||||||||||||| |||||||                     
gtgtgcatctctagcatacactccaatttcgccaaacatgtgttaaaaacatgcatttttaattccttatgaaggtgggtatgattttactcagagtatgcacctaaatgaactcaataatttatttgcatgttgg--atatatcaaattggcatctgttcagCTTGCGAACAAGTATATGAAGAGGGTTGCATCAGAACTTGATGCGTTGGAAGGCACTGAGAAAGAGCCCAATAGAGAGTTTTTGCTTCTCCAGGGTGGCA

upper sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G062738_T01 (Zea mays), 3'ss of exon 7
----------------------------------------------------------gttaacatctctagcctatgtctattgccacctttttggaccatgtagcaaatctaaaatccaaatttcatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCCACAGAGCTTGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT
                                                           ||   ||  ||     | |    |   |   |  |||||  ||| | | | | | || || | |||| || |   | |||||| ||||||||||| |||||||||| ||||| || || ||||||||||||||||||||| |||| |||||||| ||  ||||||| |||||||||||||| |||||||
gtttgcatctctagcaagcactccaattttgacaaacttgtgttaaagaaaccatgcatttttaattccttatgaaggcgggtgtgcttttacttggagtatgcaccta-tatgaactcaatattttatttg--tgtgttgg-aatagATCAAAGTGGCATCTGTCCAGCTTGCAAACAAGTATATGAAGAGGGTTGCCTCAGAACTTGATGCATTAGAAGGCACTGAGAAAGAGCCCAATAGAGAGT
















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|29630415|gb|CB635424.1|CB635424
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|58695568|gb|CK084255.1|CK084255
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|29646000|gb|CB651007.1|CB651007
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|86881810|gb|CI324099.1|CI324099
EST:     GACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGGCGAAGAAGTATATGAAGAGGGTTGC
genomic: GACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCT-GGCGAAGAAGTATATGAAGAGGGTTGC
EST: gi|86832395|gb|CI315130.1|CI315130
EST:     TACGCACTACC-GTGGATTGGCTGTCT-GTTCCGGGGTAG-TGGCAAG                         ATCAAATT-GCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: TACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|29612706|gb|CB617719.1|CB617719
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|27547352|gb|CA765429.2|CA765429
EST:     GTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: GTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|29612723|gb|CB617736.1|CB617736
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|86597114|gb|CI272709.1|CI272709
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|29613986|gb|CB618999.1|CB618999
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|18387726|gb|BM420924.1|BM420924
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCNAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|29668095|gb|CB664370.1|CB664370
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|29632488|gb|CB637497.1|CB637497
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|58609462|gb|CK037495.1|CK037495
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|86866410|gb|CI343399.1|CI343399
EST:     AGTACGGACTACCGGT-GATTGGCTGTCT-GTTCCGGGGTAGTTGGCAAG                         ATCAAATTGG-ATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|29629417|gb|CB634426.1|CB634426
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|86864001|gb|CI332927.1|CI332927
EST:     GGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: GGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
EST: gi|86893099|gb|CI333401.1|CI333401
EST:     AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC
genomic: AGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCC

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: 75 (upstream exon), 74 (downstream exon)
Score: 96

TGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATCACGCTACAGGGAGTACGGACTACCGGTGGATTGGCTGTCTGGTTCCGGGGTAGTTGGCAAGgttaacatct ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCCACAGAGCTTGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaccatgtagcaaatctaaaatccaaatttcatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCCACAGAGCTTGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT
                atctaaa  putative branch site (score: 96)
                   taaaatccaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaacatctctagcctatgtctattgccacctttttggaccatgtagcaaatctaaaatccaaatttcatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAAGAGGGTTGCCACAGAGCTTGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT