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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgccttatttctccacaaagcggcgttgcctgttttctccccttgcttagctaagtattttgattcctttctgcgcacttatatagatataacaaatttgcaccttcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAACATCGGCATGAGATTTGCCGCTACATCTACAACCACCAG

Basic information

species Zea mays
transcript GRMZM2G006937_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006937_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g35710.1 (Oryza sativa), 3'ss of exon 2
gtgcgccttatttctccacaaagcggcgttgcctgttttctccccttgcttagctaagtattttgattcctttctgcgcactt--atatagatataacaaatttgcaccttcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAACATCGGCATGAGATTTGCCGCTACATCTACAACCACCAG
                             |     |||  |    |||  ||  ||| ||||   |||| | |      | ||  | ||  || |              |   ||||||||||||| | ||||||| ||||||||||||| |   |||||||||| ||||||| |||   ||||| || ||||||||||| ||||| |||
----------------------------gtattaatttgatttttttggctaattaa-tattaatattcatgttcaattatttcgagattaatttctagtgacctagtttctgtatgcagATATTTTCTTTGTATGCCACTGGATCACTGGACACTGTCATATCATCAGAACACCGGAGGGAGATATGTCGCTACATCTATAACCATCAG
















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|148932439|gb|EC876149.2|EC876149
EST:     GGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTG                         ATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAA
genomic: GGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTGgtgcgcctta ... tcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAA
EST: gi|211012103|gb|FL418129.1|FL418129
EST:     GGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTG                         ATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAA
genomic: GGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTGgtgcgcctta ... tcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAA
EST: gi|211518858|gb|FL413399.1|FL413399
EST:     GGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTG                         ATATTTGCCTTGTATGTCACTGGATCACTGA
genomic: GGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTGgtgcgcctta ... tcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGA

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: 43 (upstream exon), 49 (downstream exon)
Score: 61

CTCCTTGAGGTCGGCTCTGGACCAGTTCTCTTCACTGCAAGCCAGCGATGGGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTGgtgcgcctta ... tcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAACATCGGCATGAGATTTGCCGCTACATCTACAACCACCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 60

CTCCTTGAGGTCGGCTCTGGACCAGTTCTCTTCACTGCAAGCCAGCGATGGGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTGgtgcgcctta ... tcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAACATCGGCATGAGATTTGCCGCTACATCTACAACCACCAG


Block sizes: 30 (upstream exon), 37 (downstream exon)
Score: 3

CTCCTTGAGGTCGGCTCTGGACCAGTTCTCTTCACTGCAAGCCAGCGATGGGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTGgtgcgcctta ... tcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAACATCGGCATGAGATTTGCCGCTACATCTACAACCACCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 169

CTCCTTGAGGTCGGCTCTGGACCAGTTCTCTTCACTGCAAGCCAGCGATGGGCACTGGCCTGGTGATTTCAGCGGGATTATGTTCATCATGCCTGGTTTGgtgcgcctta ... tcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAACATCGGCATGAGATTTGCCGCTACATCTACAACCACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattcctttctgcgcacttatatagatataacaaatttgcaccttcatatgcagATATTTGCCTTGTATGTCACTGGATCACTGAATGTTGTCATATCACCAGAACATCGGCATGAGATTTGCCGCTACATCTACAACCACCAG
                          atataac  putative branch site (score: 169)
                                        caccttc  putative PPT
                acttatatagatataa  TA-rich tract