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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatgggaatctatatatgtttttcaatacttaatgatgtaatttcttagtaacatgtttccttgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCGTAGGGCCAAATGTTTGTTGTGTATTTAGTTTTCATTGTCTAA

Basic information

species Zea mays
transcript GRMZM2G119725_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119725_T04 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 9
gtgagatgg-gaatctatata-tgtttttcaatacttaatgatgtaatttcttagtaacat---------gtttccttgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCGTAGGGCCAAATGTTTGTTGTGTATTTAGTTTTCATTGTCTAA
|||||  |  ||||| ||||  | || ||||||  |||||  |       ||   ||| ||           ||  || ||  ||||||| ||||||||||| |||||||||||||||||||| ||||| ||||||||||||||                                           
gtgagccgctgaatccatatggttttattcaatgattaatcgttggccacctatataagattcttgagtaacttttttcttcaacagAGTTACTGAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGC-------------------------------------------
















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|14245115|gb|BG873697.1|BG873697
EST:     GGACTAACATGGCAAATGACTAAACGGCGTGGTGACCAGGAAGTTCACAA                         AGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATG
genomic: GGACTAACATGGCAAATGACTAAACGGCGTGGTGACCAGGAAGTTCACAAgtgagatggg ... tgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATG
EST: gi|32805780|gb|CD958014.1|CD958014
EST:     GGACTAACATGGCAAATGACTAAACGGCGTGGTGACCAGGAAGTTCACAA                         AGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATG
genomic: GGACTAACATGGCAAATGACTAAACGGCGTGGTGACCAGGAAGTTCACAAgtgagatggg ... tgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATG

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: 49 (upstream exon), 49 (downstream exon)
Score: 255

TTAGAAAGCATGGGTTGGAAATCTCTCAGCCTGGTTTGCAACCTGATAGAGGACTAACATGGCAAATGACTAAACGGCGTGGTGACCAGGAAGTTCACAAgtgagatggg ... tgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCGTAGGGCCAAATGTTTGTTGTGTATTTAGTTTTCATTGTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

TTAGAAAGCATGGGTTGGAAATCTCTCAGCCTGGTTTGCAACCTGATAGAGGACTAACATGGCAAATGACTAAACGGCGTGGTGACCAGGAAGTTCACAAgtgagatggg ... tgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCGTAGGGCCAAATGTTTGTTGTGTATTTAGTTTTCATTGTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 356

TTAGAAAGCATGGGTTGGAAATCTCTCAGCCTGGTTTGCAACCTGATAGAGGACTAACATGGCAAATGACTAAACGGCGTGGTGACCAGGAAGTTCACAAgtgagatggg ... tgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCGTAGGGCCAAATGTTTGTTGTGTATTTAGTTTTCATTGTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

TTAGAAAGCATGGGTTGGAAATCTCTCAGCCTGGTTTGCAACCTGATAGAGGACTAACATGGCAAATGACTAAACGGCGTGGTGACCAGGAAGTTCACAAgtgagatggg ... tgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCGTAGGGCCAAATGTTTGTTGTGTATTTAGTTTTCATTGTCTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttcaatacttaatgatgtaatttcttagtaacatgtttccttgttacacagAGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCGTAGGGCCAAATGTTTGTTGTGTATTTAGTTTTCATTGTCTAA
                             tagtaac  putative branch site (score: 263)
                                       tttccttgtt  putative PPT
            ttaatgatgtaattt  TA-rich tract