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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctgaccttgttcatatcggtttctttgttttgtagtcagttttgctgtgcagagttactcttctggtttgcctaattttaaaggaaaaaaaactttacag

Basic information

species Zea mays
transcript GRMZM2G017853_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017853_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g26920.2 (Oryza sativa), 5'ss of exon 7
GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctgaccttgt--tcatatcggtttctttgttttgta-gtcagttttgctgtg---cagagttactcttctggtttgcctaattt-taaaggaaaaaaaactttacag-----------
|||||||| ||||||||  | || || |||||||||||||   || ||||||| ||| |||| |||||||| ||||| |||||||||| | ||||   ||  |  |  |  |   || |||||||  || |||   || ||||||   ||    | | ||  | | |   |   | | | ||   ||| ||| |||||             
GATGCTGCTTCCCTTGCAATTGCCATAATGAAAAAGGGACACAGGGGTCGAATCTTTTTGGGCTGTGACAATAAGCCTCTTTCCAGgtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcag
















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|211291636|gb|FL460652.1|FL460652
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|74233404|gb|DT641318.1|DT641318
EST:     GGACTGCGGAGTCGAATATTTTTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|76927172|gb|DV171164.1|DV171164
EST:     GGACTGCGGAGTGGAATATTTTTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|18177348|gb|BM378558.1|BM378558
EST:     GGACTGCGGAGTCGAATATTTATGGGCTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|71308383|gb|DR790420.1|DR790420
EST:     CGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: CGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|71310881|gb|DR791743.1|DR791743
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|78089273|gb|DV517647.1|DV517647
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|211289510|gb|FL460651.1|FL460651
EST:     GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAACCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|91051135|gb|EB161553.1|EB161553
EST:     GGACTGGGGAGTGGAATATTTTTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
EST: gi|78085441|gb|DV513834.1|DV513834
EST:     GGAATGGGGAGTGGAATATTTTTGGGTTGTGACAACAAGCCCCTTTCCAG                         GCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT
genomic: GGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTT

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: 163

GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTTTGGAGGCTTTACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTTTGGAGGCTTTACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTTTGGAGGCTTTACTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAGgtaactgctg ... aactttacagGCAAGAAATAATGGATGCTGTTAACAATAGTGGAAAATTTGACACGAAGTTTGGAGGCTTTACTG