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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatctgcttgacaaccatactcatttgaacttcatcactactatattgtgctttgagaactattgtcatcagttaaatttacatgaaactggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA

Basic information

species Zea mays
transcript GRMZM2G015324_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015324_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g41510.1 (Oryza sativa), 3'ss of exon 3
gtatgcatctgcttgacaaccatactcatttgaacttcatcactac-tatattg--tgctttgag-----aactattgtcatcagtt-aaatttacatgaaactggcct--cagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA
|||| ||||| |||  ||||||| |||| ||    |   | | ||  |||  ||  |||||| ||     | ||  |   |||| || |||||||||   ||  | |||  ||||||||||||||||| ||||| ||||||||||| | ||| || |||||||||||||| |||||| ||||||| ||||||||||| ||||||||||| || |
gtatccatctccttatcaaccattctcacttaggttctgttagtaaatattctgagtgctttcaggcacaaccttattctatcacttgaaatttacacagaatggaccttgcagATATTTGACCTTTTTGATGTGAAGAAAAGGGGGGTCATCGACTTTGGTGACTTTGTTCGAGCTTTAAATGTATTTCATCCAAACATCCCAATGGAAGAGA

upper sequence: GRMZM2G015324_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcatctgcttgacaaccatactcatttgaacttcatcactactatattgtgctttga-----gaactattgtc--atcagttaaatttacatgaaactggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA
         |||    ||| |||  |  |||  ||    | | ||||    | || |||||     |||| ||| |   |||||  |||||   || |         ||||| ||||| ||||| ||||| |||   | ||| | |||||||||||||||||||||| |  | |||||||| || |||||||||  ||||   || || |
--------atgcactgcaagcattattcttttcaccatttaaatacttctatttgttttgaaagtggaacaattttttaatcag--aaattgggatcattgaacttgcagATCTTTGATCTTTTTGATGTTAAGCGGAAGGGAGTCATTGATTTTGGTGACTTTGTCAGGTCACTAAATGTTTTCCATCCAAATGCCCCACAAGAAGACA

upper sequence: GRMZM2G015324_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0236g00150.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcatctgcttgacaaccatactcatttgaacttcatcactactatat----tgtgctttgagaactattgtcatcagttaaatttacatgaaactggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA
  ||||| ||||   |  |  || ||  |    | || |  ||| |||| |    ||   || ||  | | || | |||||  |||||   || |         ||||| ||||| ||||| ||||| |||   | ||| | |||||||||||||||||||||| |  | |||||||| || |||||||||  ||||   || || |
--atgca-ctgc--aagcattattcttttcaccatttaaatacttctatttgttttgaaattggaataattttttaatcag--aaattgggatcattaaacttgcagATCTTTGATCTTTTTGATGTTAAGCGGAAGGGAGTCATTGATTTTGGTGACTTTGTCAGGTCACTAAATGTTTTCCATCCAAATGCCCCACAAGAAGACA

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|38229501|gb|CF919814.1|CF919814
EST:     AGTTAGCATTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCTAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGAC
genomic: AGTTAGCATTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCTAATCGGgtatgcatct ... ctggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGAC




















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: 132

GAAGAATTCCAGTTAGCATTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCTAATCGGgtatgcatct ... ctggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

GAAGAATTCCAGTTAGCATTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCTAATCGGgtatgcatct ... ctggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GAAGAATTCCAGTTAGCATTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCTAATCGGgtatgcatct ... ctggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

GAAGAATTCCAGTTAGCATTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCTAATCGGgtatgcatct ... ctggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtgctttgagaactattgtcatcagttaaatttacatgaaactggcctcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGCCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGATGAAA
                             ttaaatttacatgaaa  TA-rich tract