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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttccatctctaattcctctattttcttctatgttctcaagtgagctcatttggtaatgcaaccatatcttttcatttccatgttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT

Basic information

species Zea mays
transcript GRMZM2G068212_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 3
gtaagtgtttccatctctaattcctctattttcttctatgttctcaagtgagctcatttggtaatgcaaccat-atcttttcatttccatgttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT
|||||| |||  |||| |     |||  | |  || ||  || | |  |  |    | |   |    || | | |   |   |||||||||  ||||||||||||||||||||||||| ||||| | |||||||| |||||||| ||  ||||  | ||||| ||||||||||| ||||| |||||||| || || |||||
gtaagtatttatatcttttgcaactcc-tgtctttgtagttttttatatttgtatgtctttgagcttaatcgttagtatgctatttccatgg-ctgaacagACACAGGCTTTGTCCCGCTATTTGTCTATGCAATTTTTGGCTCATCGAGACAGTTGGCAGTGGGTCCAGTGGCTCTTGTCTCTCTTCTAGTTTCTAATGT

upper sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 2
gtaagtgtttccatctctaattcctctattt---tcttctatgttctcaagtgagctcatttg-gtaatgcaaccatatcttt-tcatttccatgttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT
     | | | ||| |  |  |  | ||| |   || || ||||| |       |    ||||  ||||||   | |||   | | |||||  | | |     |||| | || ||||| ||  ||||| ||||||| |||||||| || || || || || |||||||||||||||||| | ||||||||  | || || |||||
-----tttctacattttcatgttatttatatgcatcatcaatgttttacgtcctgaaattttgtataatgcctgcttattgatgttatttctctttgcaaggaagACTCTGGTTTTGTGCCCCTATTTGTATATGCCATATTTGGGTCTTCTCGCCAGCTTGCAGTAGGTCCAGTGGCATTGGTTTCTCTCTTGGTCTCTAATGT
















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|76912515|gb|DV164770.1|DV164770
EST:     GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCT                         ACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
genomic: GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
EST: gi|88753142|gb|DY537283.1|DY537283
EST:     GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCT                         ACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
genomic: GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
EST: gi|149043278|gb|EE047338.2|EE047338
EST:     GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCT                         ACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
genomic: GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
EST: gi|211475234|gb|FL335034.1|FL335034
EST:     GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCT                         ACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
genomic: GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
EST: gi|71440768|gb|DR821818.1|DR821818
EST:     GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCT                         ACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
genomic: GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
EST: gi|71301647|gb|DR786892.1|DR786892
EST:     GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTACGGGCTCT                         ACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
genomic: GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
EST: gi|211197944|gb|FL332584.1|FL332584
EST:     GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCT                         ACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
genomic: GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
EST: gi|78086796|gb|DV515189.1|DV515189
EST:     GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCT                         ACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC
genomic: GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGAC

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), 44 (downstream exon)
Score: 43

GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 87

GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 66

GCAATGTCATATGCAAAGCTGGCTGGGCTGCACCCAATTTATGGGCTCTgtaagtgttt ... ttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgagctcatttggtaatgcaaccatatcttttcatttccatgttctgaacagACACAGGCTTTGTCCCGTTATTTATATATGCAATATTTGGCTCGTCACGACAACTAGCAGTAGGTCCAGTGGCACTTGTTTCTCTTCTTGTATCCAATGT
                          atatcttttcattt  TA-rich tract