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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTTGGACTGGAATGAGAACTGTGCGGTACTTCGATGGGAGGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcattggatgtgtagtcaaatgagctgtactgcagagcatgcagttgagctggatctatttcccagttttggtggatgttcctctttgagggaa...

Basic information

species Zea mays
transcript GRMZM2G110834_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110834_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 5'ss of exon 9
GTATTTGGACTGGAATGAGAACTGTGCGGTACTTCGATGGGAGGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcattggatgtgtagtcaaatga-gctgtactgcagagcatgcagttgagctggatctatttcccagttttggtggatgttcctctttgagggaa-
|||||||| |||||||||  |||||| | ||||| |||||||||||||| ||||||||||||||||| || |||||||| ||||||||||||||  | ||||| |||||  ||   ||||| | ||  | ||| |||||   || |   |  |  | | |     ||||||    ||| ||  ||| | | |  
GTATTTGGGCTGGAATGAAGACTGTGAGATACTTTGATGGGAGGACATATGAATGGGTTGGTTTGAGTCGTCAACCCAATATTATCAGTAAGgtatgctcattagatgtcaaggggaatgaagttgcccagcaaagcatatggtggcattatacttttctttt--ttttggcatctgtcccatttttatgcagt
















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|60397677|gb|DN230493.1|DN230493
EST:     GGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAG                         GTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAG
genomic: GGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcat ... ttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAG
EST: gi|91869156|gb|EB400279.1|EB400279
EST:     GGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAG                         GTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAG
genomic: GGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcat ... ttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAG
EST: gi|74231927|gb|DT639841.1|DT639841
EST:     GGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAG                         GTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAG
genomic: GGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcat ... ttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAG
EST: gi|71318559|gb|DR796040.1|DR796040
EST:     GGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAG                         GTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAG
genomic: GGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcat ... ttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAG

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: 43 (upstream exon), 49 (downstream exon)
Score: 110

GTATTTGGACTGGAATGAGAACTGTGCGGTACTTCGATGGGAGGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcat ... ttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAGTGGCACCCTACGCGGGGTCCTTGGAGATTCATCCAGGTGCTGAGCCTCT


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

GTATTTGGACTGGAATGAGAACTGTGCGGTACTTCGATGGGAGGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcat ... ttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAGTGGCACCCTACGCGGGGTCCTTGGAGATTCATCCAGGTGCTGAGCCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

GTATTTGGACTGGAATGAGAACTGTGCGGTACTTCGATGGGAGGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcat ... ttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAGTGGCACCCTACGCGGGGTCCTTGGAGATTCATCCAGGTGCTGAGCCTCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 69

GTATTTGGACTGGAATGAGAACTGTGCGGTACTTCGATGGGAGGACATACGAATGGGTTGGTTTGAGCCGCCAACCCAACATTATCAGTAAGgtgcgttcat ... ttctccttagGTAAAAAGGATGCTGGGACAGTTCACACCAGCGCAGTGGGACAAGGATGAGTGGCACCCTACGCGGGGTCCTTGGAGATTCATCCAGGTGCTGAGCCTCT