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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgatcttcttgtctcatatttacagttcaactgttcaagttgcaattgttcaacaattcacagtcattttttattatttattgtttcttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG

Basic information

species Zea mays
transcript GRMZM2G037683_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 10
gtgctgatcttct-----tgtctcatatttacagttcaa-ctgttcaagttgcaattgttcaacaattcacagtcattttttat---tatttattgtttcttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG
||   |||||  |         | || ||||   ||    ||  |   ||    ||| |||  ||  |   |   || | | ||    || |||| ||||||  ||||||| |||||||| |||||||||||||| ||||| || ||||||||||||||||||||||||
gtatagatctcttgtatacaattaatctttatgtttttttctacttccgtatatattattctgcatgttgtataaatgtctcatattcatgtattatttcttgatgtagGTGTGGGATACGAAAACAACAGATTGTTTGCAAACATTCAAGCCACCACCTCCTTTGAGG
















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|211475898|gb|FL358552.1|FL358552
EST:     CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAG                         GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCT
genomic: CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCT
EST: gi|67019283|gb|CO448032.1|CO448032
EST:     CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAG                         GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCA-GCCACCACCT
genomic: CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCT
EST: gi|22521028|gb|BU079839.1|BU079839
EST:     CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAG                         GTCTGGGATACTAAAACAACAGATT
genomic: CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATT
EST: gi|211442071|gb|FL307771.1|FL307771
EST:     TTGTACTGTTAAG                         GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCT
genomic: TTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCT
EST: gi|91873183|gb|EB403140.1|EB403140
EST:     CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAG                         GTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTTCA-GCCACCACC
genomic: CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTT-CAAGCCACCACC
EST: gi|211277652|gb|FL322062.1|FL322062
EST:     CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTANC                         GNCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCT
genomic: CTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCT

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: 119

GCTGAAAGAATTTCGAGGTCATTCTTCATATGTAAATTATGCCATCTTCACTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 65

GCTGAAAGAATTTCGAGGTCATTCTTCATATGTAAATTATGCCATCTTCACTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 69

GCTGAAAGAATTTCGAGGTCATTCTTCATATGTAAATTATGCCATCTTCACTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 24

GCTGAAAGAATTTCGAGGTCATTCTTCATATGTAAATTATGCCATCTTCACTACTGACGGTAGCCGTGTCATTACAGCTTCCAGTGATTGTACTGTTAAGgtgctgatct ... cttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaattgttcaacaattcacagtcattttttattatttattgtttcttattgtagGTCTGGGATACTAAAACAACAGATTGCTTGCATACTTTCAAGCCACCACCTCCTTTGAGG
                                       ttgtttctt  CT-rich tract
                    agtcattttttattat  TA-rich tract