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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCGGGTTTTATTTACACCCTGCTGAAGGCTCGCCTGCACCAAACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgttttcagaaatcaatgatacacagcaatgcaagataccatcaaacggtgaatcctctagcacacaaccatctcagtgggtggggattttgtg...

Basic information

species Zea mays
transcript GRMZM2G167999_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os12g06810.3 (Oryza sativa), 5'ss of exon 6
ATGCGGGTTTTATTTACACCCTGCTGAAGGCTCGCCTGCACCAAACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgttttcagaaatcaatgatacacagcaatgcaagataccatcaaacggtgaatcctctagcacacaaccatctcagtgggtggggattttgtg-
 || || || || || || ||||||||||| || |||||||| |||||||| |||||||| ||||||||||||||||||||||| |||||||| |||||||   ||   || |   ||||| | |        |  || || |  | | ||      |||| ||| |   ||||        |      |  |  
GTGTGGATTCTACTTGCATCCTGCTGAAGGGTCACCTGCACCGAACATAACACAAGGGAAACTTAGTGCTCCACGGATATTGCGGATTCACAAAgtaagattgctttgaaatttcttgatatatactcccaatatgtagcaacctaggatgggattcctaggaca-acgaatctggacataagaacccatcctag
















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|71317699|gb|DR795606.1|DR795606
EST:     ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAG                         GTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
genomic: ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
EST: gi|6056606|gb|AW091011.1|AW091011
EST:     ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAG                         GTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
genomic: ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
EST: gi|67025265|gb|CO454014.1|CO454014
EST:     ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAG                         GTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
genomic: ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
EST: gi|6020795|gb|AW065723.1|AW065723
EST:     ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAG                         GTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
genomic: ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
EST: gi|211189104|gb|FL252863.1|FL252863
EST:     ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAG                         GTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
genomic: ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
EST: gi|32919061|gb|CF023873.1|CF023873
EST:     ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAG                         GTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
genomic: ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
EST: gi|211234744|gb|FL433588.1|FL433588
EST:     ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAG                         GTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA
genomic: ACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGA

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), 48 (downstream exon)
Score: 119

ATGCGGGTTTTATTTACACCCTGCTGAAGGCTCGCCTGCACCAAACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGAGGCTCTGATGCGTTTGTTATGGGATTGAGTTCTGCTCAATCACAGCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

ATGCGGGTTTTATTTACACCCTGCTGAAGGCTCGCCTGCACCAAACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGAGGCTCTGATGCGTTTGTTATGGGATTGAGTTCTGCTCAATCACAGCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

ATGCGGGTTTTATTTACACCCTGCTGAAGGCTCGCCTGCACCAAACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGAGGCTCTGATGCGTTTGTTATGGGATTGAGTTCTGCTCAATCACAGCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

ATGCGGGTTTTATTTACACCCTGCTGAAGGCTCGCCTGCACCAAACATAACTCAAGGGAAGCTTAGTGCTCCACGGATATTGCGAATTCACAAGgtaagatgtt ... cattgtacagGTAGCTAACTATGTGGTTGAGAAACTCGTTCTTGACAAACCATTGGATGGAGGCTCTGATGCGTTTGTTATGGGATTGAGTTCTGCTCAATCACAGCTCT