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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttttgtgcttccatagtttcattctggaatcatgtgatatattgtgctgccttatttagttgtggtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG

Basic information

species Zea mays
transcript GRMZM2G173777_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173777_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 10
gcaa-gttttgtgcttccatagtttcattctggaatcatgtgatatattgtgctgccttatttagttgtggtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG
|||| | | ||| |||| || ||   ||| |  || |   |  | |     | |||||||||      | | ||||| |||||||||||||||||||||||||||||||  |||||||||||||||| |||||||||||||| || |||||||| ||||| ||||| ||||||
gcaaagctctgttcttctattgtaggattattaaaac---tattttgcca-gttgccttattagacactag-cattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG

upper sequence: GRMZM2G173777_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G35510.1 (Glycine max), 3'ss of exon 8
gcaagttttgtgcttccatagtttcattctggaatcatgtgatatattgtgctgccttatttagttgtggtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG
           |     |||  | |  |     | |||    | ||||      |  || |||  | |         ||||||||||||||||  | ||||| ||||| ||||||||||||||||||||||||||||| || || || ||| | || || || || || |||
-----------gtaagtataactcctgtacctga-cattgactttattaatgctctgtaattaactatatgtgcaatcagGTCCAACTCATGTGCTTGTTGTCCGTGGATTGGATGAAAATGCTGATGAGGAAATGCTCCGCTATGAGTTTTCCAAACATGCTCCGATTAAG

upper sequence: GRMZM2G173777_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA16G18030.1 (Glycine max), 3'ss of exon 8
gcaagttttgtgcttccatagtttcattctggaatcatgtgatatattgtgctgccttatttagttgtggtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG
| |||| |    || || ||        |||  ||    || | ||||         || |||  | |         |||||||||||||||| || ||||| ||||| |||||||||||||| |||||||||||||| || || || ||| | || || || || || |||
gtaagtataa--ctcccgta-------cctgacattg-atgctttattaatgctttgtaattaactatatgtgcaatcagGTCCAACTCATGTGTTGGTTGTCCGTGGATTGGATGAAAATGCGGATGAGGAAATGCTCCGCTATGAGTTTTCCAAACATGCTCCGATTAAG

upper sequence: GRMZM2G173777_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G54230.2 (Arabidopsis thaliana), 3'ss of exon 10
------------------------------------------------------------gcaagttttgtgcttccatagt-ttcattctggaat-catgtgatatattgtgctgccttatttag-ttgtggtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG
                                                            |||| | ||  |   ||||||| ||  | ||    | ||||  ||||||      |    |||  | || |  || ||| ||||||||||||||||  | ||||| ||||| ||||||||| ||||||||||||||||||||||||| |||||| | || || || || || |||
gttctgatcagcatttttatttaagatgttttaaatttctttcttgagtcagaaacagtcgcaactgttaagg--ccatagtctttgtacttttctacatgccatatatacctaagatacattctgcttattttcttttccagGTCCAACTCATGTCCTGGTTGTACGTGGGTTGGATGAAGATGCTGATGAGGAAATGCTTCGGTATGAATTTTCCAAACATGCTCCTATCAAG

upper sequence: GRMZM2G173777_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 3'ss of exon 8
gcaagttttgtgcttccatagtttcattctggaatcatgtgatatattgtgctgcct-tatttagttgtggtcatttg----cagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG
    |||       ||||| | ||     ||| ||    | |   ||| |  |   | || || | |  | | || ||    ||||||| |  |||||||| |||||||| || |||||||||||||||||||||||||||||||| || |||||| |||| || || ||||| |||
----gttggaacactccattgcttttaattggcat-gcattaagcattatattcattgtaatttgctaagttgatatgtaatcagGTCCTATCCATGTTTTGGTTGTTCGAGGTTTGGATGAAAATGCTGATGAGGAAATGCTTCGTTATGAATTTTCTAAACATGCTCCAATCAAG

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|18649089|gb|BM497908.1|BM497908
EST:     GGAGAAGGGGATCTGAACTAG                         GTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGG
genomic: GGAGAAGGGGATCTGAACTAGgcaagttttg ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGG
EST: gi|22489941|gb|BU049864.1|BU049864
EST:     GGAGAAGGGGATCTGAACTAG                         GTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGG
genomic: GGAGAAGGGGATCTGAACTAGgcaagttttg ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGG
EST: gi|211224726|gb|FL222444.1|FL222444
EST:     CTTTGGGAGAAGGGGATCTGAACTAG                         GTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGG
genomic: CTTTGGGAGAAGGGGATCTGAACTAGgcaagttttg ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGG
EST: gi|211344311|gb|FL081282.1|FL081282
EST:     CTTTGGGAGAAGGGGATCTGAACTAG                         GTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGG
genomic: CTTTGGGAGAAGGGGATCTGAACTAGgcaagttttg ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGG

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 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 112

TGCAATGAACCTCGTACTGAGGATGCTCTTCCAGCTGATGCGACAGGTTCCGCTTCACACTTTGGGAGAAGGGGATCTGAACTAGgcaagttttg ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 73

TGCAATGAACCTCGTACTGAGGATGCTCTTCCAGCTGATGCGACAGGTTCCGCTTCACACTTTGGGAGAAGGGGATCTGAACTAGgcaagttttg ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 76

TGCAATGAACCTCGTACTGAGGATGCTCTTCCAGCTGATGCGACAGGTTCCGCTTCACACTTTGGGAGAAGGGGATCTGAACTAGgcaagttttg ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 75

TGCAATGAACCTCGTACTGAGGATGCTCTTCCAGCTGATGCGACAGGTTCCGCTTCACACTTTGGGAGAAGGGGATCTGAACTAGgcaagttttg ... tcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctggaatcatgtgatatattgtgctgccttatttagttgtggtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG
                               ttatttagtt  TA-rich tract