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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgacatgtttgtattctacccttcacattttttatggaagattttgtttatctgaaatcttgggctattttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC

Basic information

species Zea mays
transcript GRMZM2G068755_T03
intron # 42
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 44
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 43
gtttgacatgtttgtattctacccttcacattttttatggaagattttgtttatctgaaatcttgggctattttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC
|||||   | | |||| |||   || |   |  | | ||   | ||   | |   | |  | |  |||| | ||  ||||| || |||||||||||||||||||||||||||||||||||||| || || |||||||| || ||| |||| |||||||| |||||||||||||||||||
gtttg---tttgtgtactcttttctccttttgctctttgtttggttcaatgttatttatgtat-aggctgtattt-cagACTTTCCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACTCTAGATAACCTTATCACAGAGCTACTACTTTGGCTCTTAGATGAAAGGGTTCCTC

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 44
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 15
----------gtttgacatgtttgtattct-acccttcacattttttatggaaga----ttttgtttatctgaaat-------cttgggctattttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC
             | | |  | || |||||   |      | | |  ||| | ||    | || | |  |  |||        |||||  | ||||| |||||||||||||  |||   |||||||||||||| ||||||  ||| |||||||  ||||| || ||| |  | ||||||||||| ||||||||||||||||
ataaaaataaaaataaaaaatctggattcttgacaactgtactgtgcatgaaggaaatgtattatgtcacaaaaacttaactacttggagttttttg-cagACATTTCAGAATAAAAAACTTGCTCATGCTGTCAAGGAGTCTACTCTTGACAGTCTTATCACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTC
















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|67021414|gb|CO450163.1|CO450163
EST:     CTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG                         ACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
genomic: CTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
EST: gi|71317537|gb|DR795494.1|DR795494
EST:     CTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG                         ACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
genomic: CTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC

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: 46 (upstream exon), 49 (downstream exon)
Score: 239

GTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

GTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 139

GTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 119

GTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacattttttatggaagattttgtttatctgaaatcttgggctattttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTTTTAGATGAAAGGGTTCCTC
                                           ctatttt  CT-rich tract
                aagattttgtttat  TA-rich tract