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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaactgaatgcaactaattttgcatttcctgtag

Basic information

species Zea mays
transcript GRMZM2G044819_T03
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g14810.1 (Oryza sativa), 5'ss of exon 15
ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaac---------tgaatgcaactaattttgcatttcctgtag
|||||||||| | |||||| | || |||||||||||||||||||| || |||||||||||||||||||| | |||  ||||    | ||||| |  | | |||||  | | ||           | ||||||| || |||||   |   || ||
ATGGGGTTGGCTATCACGTACGGGCCTATGGGATAAGAGTCATCTGACGAGGCAAATTGAAAAgtgagtggttatggttttgcagtggtgaatattatt-ttatgagcccaaattttatctgtgtaaatgcaatta-ttttgtcctcggtgcag
















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|32834655|gb|CD974333.1|CD974333
EST:     TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|78025583|gb|DV493970.1|DV493970
EST:     TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|5713778|gb|AI943770.1|AI943770
EST:     TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|211089552|gb|FL477198.1|FL477198
EST:     CCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: -CACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|211089553|gb|FL477199.1|FL477199
EST:     TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|148967092|gb|EE018262.2|EE018262
EST:     TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|12973741|gb|BG268632.1|BG268632
EST:     TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST: gi|16917596|gb|BM073359.1|BM073359
EST:     TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA                         ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC

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: 47 (upstream exon), 49 (downstream exon)
Score: 86

ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 89

ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG