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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTACCAATAGGGTCAACCTGACACCAGTTGCACTGATGGAGGGTGGGGCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacatttatcatatcatcaccaggaatcttgaacaccacatattcatggtggctgtcttatggctcatttgacttacctatccagctagaacaga...

Basic information

species Zea mays
transcript GRMZM2G172322_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172322_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g06740.1 (Oryza sativa), 5'ss of exon 6
ATGTTACCAATAGGGTCAACCTGACACCAGTTGCACTGATGGAGGGTGGGGCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacatttatcatatcatcaccaggaatcttgaacaccacatattcatggtggctgtcttatggctcatttgacttacctatccagctagaacaga----
|||||||  |||||||||||||||||||||||||||| ||||| ||||| |||||||| ||||| || |||||  ||||||||||||||||||||||||||||| ||   |   | |||||  |  |      ||  ||| | ||| ||   || |  ||| || | | |  | |    |    |        | | |      
ATGTTACTGATAGGGTCAACCTGACACCAGTTGCACTTATGGAAGGTGGTGCATTTGCAAAAACAGTGTTTGGTGATGAACCTACCAAACCAGATTACAGgtatgtaggatatccctatcaagaatacctcagtt--acatcgcatgtttgagg-gaatgt-ttgttgttgctgtacagtgtacacttgagctgcatatttttg

upper sequence: GRMZM2G172322_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv07s0141g00390.t01 (Vitis vinifera), 5'ss of exon 6
ATGTTACCAATAGGGTCAACCTGACACCAGTTGCACTGATGGAGGGTGGGGCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgt-----atctacatt-tatcatatcatcaccaggaatcttgaacac---cacatattcatggtggctgtcttatggct-catttgact--tacctatccagctagaacaga
|||| ||  ||||  | ||  |||| ||||||||  |||||||||| || ||||| || |||||| | ||||| |||||||| || ||||||||||| ||||     |||||  || |   | ||  |      | ||  |   |      |   |||||  |  |||    | | | | ||||| |||  |  ||   |            
ATGTAACAGATAGAATAAATTTGACTCCAGTTGCTTTGATGGAGGGAGGAGCATTAGCTAAAACTCTATTTGGGAATGAACCAACAAAACCAGATTATAGgtgttctatctattttgtgcaaaattgtttggtagcattgttggcgtggataaggattcagagatgctcctgtctagatacatttaactattgtctgctc------------
















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|149037276|gb|EE155319.2|EE155319
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|211393001|gb|FL405406.1|FL405406
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|60359695|gb|DN226668.1|DN226668
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|211356738|gb|FL440505.1|FL440505
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|148956137|gb|EC901907.2|EC901907
EST:     CATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: CATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|149101004|gb|EE187101.2|EE187101
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|71319218|gb|DR796369.1|DR796369
EST:     GCATTGGCGAAAACTGTCTTTGGCAATGAACCTACCAACCCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|93017205|gb|EB642725.1|EB642725
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAACCCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|211356737|gb|FL440504.1|FL440504
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTCCCCAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCCAACCACCAATAGGACAAGTTGGTC
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCT-CCCAACCACCAATAGGACAAGTTGGTC
EST: gi|211484881|gb|FL392986.1|FL392986
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|76932106|gb|DV172946.1|DV172946
EST:     GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: GCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
EST: gi|60398346|gb|DN231162.1|DN231162
EST:     AAACCAGATTACAG                         AGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT
genomic: AAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 82

ATGTTACCAATAGGGTCAACCTGACACCAGTTGCACTGATGGAGGGTGGGGCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 280

ATGTTACCAATAGGGTCAACCTGACACCAGTTGCACTGATGGAGGGTGGGGCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

ATGTTACCAATAGGGTCAACCTGACACCAGTTGCACTGATGGAGGGTGGGGCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 212

ATGTTACCAATAGGGTCAACCTGACACCAGTTGCACTGATGGAGGGTGGGGCATTTGCGAAAACTGTCTTTGGCAATGAACCTACCAAACCAGATTACAGgtatctacat ... tttttggcagAGCTATACCTTCTGCTGTGTTCTCCCAACCACCAATAGGACAAGTTGGTCTTACTGAGGAGCAG