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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgtatcaaacttcttttttctgactgaactattgattaactaatgacacatttctggcgctttatgacttatgctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGATTTTATATTTTTGGAACCGTTTTGAG

Basic information

species Zea mays
transcript GRMZM5G814310_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 11
gtatgtgtgtatcaaacttcttttttctgactga-actattgattaactaatgacacatttctggcgctttatgacttatgc---------tttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGATTTTATATTTTTGGAACCGTTTTGAG
|||||  |  ||   |  |||||||  ||||  | | |    |  ||||| ||  | ||  ||  || | ||||||||             |||| |||||||||| || ||||| || ||||| || || || |||||||| || || |||||||||||||||||||| || |||
gtatgactacat---atgtctttttggtgacctatattggcaagaaactactggaatatc-ctatcgatatatgacttgcatatttctgtatttatcagGCTTCTCCTACCTGGCCTTTTCTGCCACCGCGGCGTTCATGCAACATCTAATTTTATATTTTTGGAACCGCTTCGAG

upper sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 13
-----gtatgtgtgtatcaaacttcttttttctgactgaactattgattaactaatgacacatttctggcgctttatgacttatgctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGATTTTATATTTTTGGAACCGTTTTGAG
       ||||| || | |   |   ||| ||| | | ||||| |||  ||||   ||| | ||     | |||  ||  | |  ||  || ||| || || ||||| ||  |     | || || ||||||||||| ||| | |||||||| || |||||||||||||||
gtaagagatgtg-gttttacgttatatttgtctcatt-aactactga--aactgcagacgcgtt-----cacttactgcataactctccac-agGTTTTTCTTATCTCGCCCTAATGACAACCGCTGCATTCATGCAACACTTAATTTTATACTTCTGGAACCGTTTTGAG
















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|211379778|gb|FL404067.1|FL404067
EST:     CTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG                         GCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAACACCTGA
genomic: CTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGgtatgtgtgt ... gctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGA
EST: gi|211054879|gb|FL422556.1|FL422556
EST:     CTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG                         GCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAACACCTGA
genomic: CTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGgtatgtgtgt ... gctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGA
EST: gi|211393234|gb|FL418031.1|FL418031
EST:     CTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG                         GCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAACACCTGA
genomic: CTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGgtatgtgtgt ... gctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGA
EST: gi|67010774|gb|CO439523.1|CO439523
EST:     CTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG                         GCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGA
genomic: CTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGgtatgtgtgt ... gctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 101

TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGgtatgtgtgt ... gctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGATTTTATATTTTTGGAACCGTTTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGgtatgtgtgt ... gctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGATTTTATATTTTTGGAACCGTTTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 107

TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGgtatgtgtgt ... gctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGATTTTATATTTTTGGAACCGTTTTGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 96

TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGgtatgtgtgt ... gctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGATTTTATATTTTTGGAACCGTTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattgattaactaatgacacatttctggcgctttatgacttatgctttaccagGCTTCTCATATCTGGCTTTCTCTGCTACGGCAGCATTCATGCAGCACCTGATTTTATATTTTTGGAACCGTTTTGAG
          aactaat  putative branch site (score: 96)
                                              ctttacc  putative PPT
       attaactaat  TA-rich tract