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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgcaatagattaaatcgtttcctccctatgaatattacagttattatatctctacttggtgagctccccgtaaaattattatccactataccgtgcatgtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG

Basic information

species Zea mays
transcript GRMZM2G124918_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124918_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 8
---------------gtaaatgcaatagattaaatcgtttcctccctatgaatattacagttattatatctctacttggtgagctccccgtaaaattattatccactataccgtgcatgtgt--------ttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG
                ||  ||  | | |||| |   |    |   |  ||  |||    || | |  | |    ||| | || ||    ||| ||     |     |||   |   | ||         | ||||||| ||||| ||||| |||||||||||||||||||| |||||||||
gtaaatgaaatattactacttgtcacacattataatttgcattttttgggatcatttt--ttgtgaggttttctgttgtttagttcgaactaatatctccttggctcataatttatttctgcaaaacgtatcacagGAATGAGAGTGCTCTGAAATTTGGATGGTTTTTCCTGTTCTACTTG
















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|14243814|gb|BG841530.2|BG841530
EST:     TGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG                         GAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG
genomic: TGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAGgtaaatgcaa ... gtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG
EST: gi|95107983|gb|EB740212.1|EB740212
EST:     TGCCCAGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG                         GAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG
genomic: TGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAGgtaaatgcaa ... gtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG
EST: gi|71766083|gb|DR964020.1|DR964020
EST:     TGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAG                         GAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG
genomic: TGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAGgtaaatgcaa ... gtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG

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: 48 (upstream exon), 28 (downstream exon)
Score: 20

GTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAGgtaaatgcaa ... gtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 295

GTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAGgtaaatgcaa ... gtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 293

GTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAGgtaaatgcaa ... gtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG


Block sizes: 46 (upstream exon), 34 (downstream exon)
Score: 88

GTCCTAAAATATGGTTTCTCGCAATCATATACTTCATTCTTGGATGCCCCGGCGCCTACTACCTTTGGTACCGGCCACTATACCGTGCCATGAGgtaaatgcaa ... gtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttggtgagctccccgtaaaattattatccactataccgtgcatgtgtttacagGAACGAGAGCGCTCTTAAATTTGGATGGTTTTTCCTATTCTACTTG
                 taaaattattatcca  TA-rich tract