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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagtcttaactacgtaagttcctaatagattaatctatgtgaagcatggaaaggagtttaatatcgccactgggttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTCGAAGGCCTAGGTTCACCATTGTCATGGGATCACATCACCAATCAG

Basic information

species Oryza sativa
transcript LOC_Os02g14110.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g14110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 7
----------------gtaagaagtcttaac-tacgtaagttcctaatagattaa-tctat-----gtgaagcatggaaaggagt--ttaatatcgccactgggttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTCGAAGGCCTAGGTTCACCATTGTCATGGGATCACATCACCAATCAG
                  |  |   |||||  | | ||  |  |||   | |||| |||||     |||||  | | ||    ||  | || | ||| | ||  |||| |||||||||||||||||| |||||||||||||||||||||||   ||||||||| |||   ||||||||||| |||||||||||||| ||||| ||||||
gtaaatcgtgaatcctacataagtacttaatgttcttatatggctaggtggttaaatctattgttagtgaataaagaaagaatgtggtcaaca-cgctattga-ttgtttcagGGTATGGCTGATCGTATCATTGGAATGCGGAAGGCACTTAAGGAAAATCTTGAAAAGCTAGGTTCACCTTTGTCATGGGATCATATCACTAATCAG
















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|86492150|gb|CI134783.1|CI134783
EST:     GTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: GTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|86859475|gb|CI278876.1|CI278876
EST:     TATGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|33808186|gb|CF329982.1|CF329982
EST:     TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|87010181|gb|CI279278.1|CI279278
EST:     TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|88224138|gb|CI223987.1|CI223987
EST:     TTTATGGTTGAAAGAGNTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|88245936|gb|CI245785.1|CI245785
EST:     TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|29689346|gb|CB685621.1|CB685621
EST:     TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|29683411|gb|CB679686.1|CB679686
EST:     GTTGAAAGAGGTCAAC                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: GTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|86494910|gb|CI137543.1|CI137543
EST:     TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|86494684|gb|CI137317.1|CI137317
EST:     TGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|287234|gb|D16037.1|D16037
EST:     TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|86496294|gb|CI138927.1|CI138927
EST:     GTTTATGGTTGAAAGAGGTCAAG                         GGTATGNCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: GTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
EST: gi|86494861|gb|CI137494.1|CI137494
EST:     TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAG                         GGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC
genomic: TAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTC

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), 75 (downstream exon)
Score: 58

AAGGCCAATGTACAGCAACCCACCTGTTCATGGTGCACTGGTTGTCTCCATAATCCTTAATGATCCAGAATTAAAGAGTTTATGGTTGAAAGAGGTCAAGgtaagaagtc ... gttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTCGAAGGCCTAGGTTCACCATTGTCATGGGATCACATCACCAATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatctatgtgaagcatggaaaggagtttaatatcgccactgggttgtctcagGGTATGGCTGATCGAATCATTGGAATGCGGAAGGCACTCCGGGAAAATCTCGAAGGCCTAGGTTCACCATTGTCATGGGATCACATCACCAATCAG
                                              ttgtctc  CT-rich tract
                          agtttaatat  TA-rich tract