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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgcgctctccagtgcactgcaattcgctcggaatcttccctgaatgcttctctgtggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT

Basic information

species Zea mays
transcript GRMZM2G100260_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100260_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 1
gtgagcgcgctctccagtgc-act-gcaattcgctcggaa------------tcttccctgaatgct---tctctgtggg-------gtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT
||||||| | || ||  | | ||| || |       |||             |  | ||||| || |   |  | |||||       || |||||| ||||||||  | ||||| ||||| ||||| || |||||||| || ||||||||||||||||| ||||| ||| ||||||| ||||||||
gtgagcgggttcccctctcccactcgctagctaggaggaggaggcgagcggctgattcctgattggttggttcccgtgggttttttggttgcagGTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACAT
















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|211144459|gb|FL048070.1|FL048070
EST:     GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAG                         GTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTCCTCGTC
genomic: GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
EST: gi|211144465|gb|FL048076.1|FL048076
EST:     GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAG                         GTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
genomic: GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
EST: gi|211144466|gb|FL048077.1|FL048077
EST:     GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAG                         GTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
genomic: GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
EST: gi|211144461|gb|FL048072.1|FL048072
EST:     GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAG                         GTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
genomic: GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
EST: gi|211144462|gb|FL048073.1|FL048073
EST:     GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAG                         GTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
genomic: GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
EST: gi|14701176|gb|BI233594.1|BI233594
EST:     GACACAGGATGAGGGCTG-GGTGCAGCGCGTCCTCTCGGCCAGTGTCGAG                         GTGCG-GGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGT
genomic: GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGT-CGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGT
EST: gi|211144469|gb|FL048080.1|FL048080
EST:     GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAG                         GTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC
genomic: GACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTC

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), 49 (downstream exon)
Score: 25

GCGACTCGTCCGGTCGTCCCTCAGCACTGTGCTTGGCGGACGCAGGACAAGACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 18

GCGACTCGTCCGGTCGTCCCTCAGCACTGTGCTTGGCGGACGCAGGACAAGACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 18

GCGACTCGTCCGGTCGTCCCTCAGCACTGTGCTTGGCGGACGCAGGACAAGACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

GCGACTCGTCCGGTCGTCCCTCAGCACTGTGCTTGGCGGACGCAGGACAAGACACAGGATGAGGGCTGTGGTGCAGCGCGTCCTCTCGGCCAGTGTCGAGgtgagcgcgc ... ggggtcgcagGTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACAT