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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtaagtgctcttttcactttttactttagatggtctggaaggttaatttgacctttacttcctatttcttacagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATT

Basic information

species Zea mays
transcript GRMZM2G045241_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045241_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 2
gtaagtagtaagtgctcttttcactttttactttagatggtctggaaggttaatttgacctttacttcctatttctta-cagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATT
|| || ||||| |     |  |   |  || | |   | |  ||     | | ||    | |  | ||  |||||||  |||||||||| ||||| || ||||||| ||||| ||||||||||||||||||| ||||| |||    ||||| |||||||||
gtcagcagtaattatc--tcgcgaatcatattatttgttgcgtgcgcactaatttctgacatggcatctaatttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAGGGCTTATAACACTGAAACAAATGAAATT
















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|71316934|gb|DR795151.1|DR795151
EST:     TCAGTGATTTTTGGCAAACACTCTTTGGTTAGATTAAGAATCATGGAAAG                         GTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTAT
genomic: TCAGTGATTTTTGGCAAACACTCTTTGGTTAGATTAAGAATCATGGAAAGgtaagtagta ... tttcttacagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTAT
EST: gi|166421745|gb|EG232073.1|EG232073
EST:     CAAACACTCTTTGGTTAGATTAAGAATCATGGAAAG                         GTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTAT
genomic: CAAACACTCTTTGGTTAGATTAAGAATCATGGAAAGgtaagtagta ... tttcttacagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTAT

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: 246

CTGAGTTTTGAAGGTGGCGAGGGATCTTTGCTGCGGGGTTCTATTTGTTCTCAGTGATTTTTGGCAAACACTCTTTGGTTAGATTAAGAATCATGGAAAGgtaagtagta ... tttcttacagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 187

CTGAGTTTTGAAGGTGGCGAGGGATCTTTGCTGCGGGGTTCTATTTGTTCTCAGTGATTTTTGGCAAACACTCTTTGGTTAGATTAAGAATCATGGAAAGgtaagtagta ... tttcttacagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CTGAGTTTTGAAGGTGGCGAGGGATCTTTGCTGCGGGGTTCTATTTGTTCTCAGTGATTTTTGGCAAACACTCTTTGGTTAGATTAAGAATCATGGAAAGgtaagtagta ... tttcttacagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 265

CTGAGTTTTGAAGGTGGCGAGGGATCTTTGCTGCGGGGTTCTATTTGTTCTCAGTGATTTTTGGCAAACACTCTTTGGTTAGATTAAGAATCATGGAAAGgtaagtagta ... tttcttacagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactttagatggtctggaaggttaatttgacctttacttcctatttcttacagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATT
                          atttgac  putative branch site (score: 265)
                                cctttacttcctattt  CT-rich tract
                       ttaatttga  TA-rich tract