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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGAATGCAGCAAAGAGTCCAATCATTGCTTCAGCCTGGCTTACAGTTGCTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtactttagttcagtgatggaacagacactcgttcttctccatttggatcttctttttcccatctgatatatatcatttctaaaatgtaacag

Basic information

species Zea mays
transcript GRMZM5G856598_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856598_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g63290.2 (Oryza sativa), 5'ss of exon 6
TCTGAATGCAGCAAAGAGTCCAATCATTGCTTCAGCCTGGCTTACAGTTGCTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtacttta-----gttcagtgatggaacagaca-------ctcgttcttctcc---atttggatcttctttttcccatctgatatatatcatttctaaaatgtaa-cag
 || |||||||||||||||||| |||| ||||| || ||||||||  | ||||| || ||||| ||||| || |||||||||||  |||||||||| |||||| ||||     |||  |  ||| |  | |            ||| | | ||   ||||||||  |||||| ||| ||||||| |  ||||| ||||| | | | |||
ACTAAATGCAGCAAAGAGTCCAGTCATCGCTTCTGCTTGGCTTACTATCGCTGTAGGTTTGAAGTCCTTTGGTCACTCAGGTTTTCTAGTAAATCTTCAGgtattttacactcgttatgccatgtactatatgaatcttttctgttttccccctcaatttggattctcttttaccc-tctgatacaattcattcctaaacttttatcag
















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|71435181|gb|DR816231.1|DR816231
EST:     CTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAG                         GAGATTGCCCCACAATATGCTGGAGTCCTACATG
genomic: CTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtactttagt ... aatgtaacagGAGATTGCCCCACAATATGCTGGAGTCCTACATG
EST: gi|32859895|gb|CD999576.1|CD999576
EST:     GGTTTCTTAGTAAATCTACAG                         GAGATTGCCCCACAATATGCTGGAGTCCTACATG
genomic: GGTTTCTTAGTAAATCTACAGgtactttagt ... aatgtaacagGAGATTGCCCCACAATATGCTGGAGTCCTACATG
EST: gi|7145129|gb|AW506610.1|AW506610
EST:     CTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAG                         GAGATTGCCCCACAATATGCTGGAGTCCTACATG
genomic: CTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtactttagt ... aatgtaacagGAGATTGCCCCACAATATGCTGGAGTCCTACATG
EST: gi|32921298|gb|CF026110.1|CF026110
EST:     CTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAG                         GAGATTGCCCCACAATATGCTGGAGTCCTACATG
genomic: CTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtactttagt ... aatgtaacagGAGATTGCCCCACAATATGCTGGAGTCCTACATG

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), 34 (downstream exon)
Score: 102

TCTGAATGCAGCAAAGAGTCCAATCATTGCTTCAGCCTGGCTTACAGTTGCTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtactttagt ... aatgtaacagGAGATTGCCCCACAATATGCTGGAGTCCTACATG


Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 62

TCTGAATGCAGCAAAGAGTCCAATCATTGCTTCAGCCTGGCTTACAGTTGCTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtactttagt ... aatgtaacagGAGATTGCCCCACAATATGCTGGAGTCCTACATG


Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 108

TCTGAATGCAGCAAAGAGTCCAATCATTGCTTCAGCCTGGCTTACAGTTGCTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtactttagt ... aatgtaacagGAGATTGCCCCACAATATGCTGGAGTCCTACATG


Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 90

TCTGAATGCAGCAAAGAGTCCAATCATTGCTTCAGCCTGGCTTACAGTTGCTGTTGGATTGAAATCCTTCGGCCACTCAGGTTTCTTAGTAAATCTACAGgtactttagt ... aatgtaacagGAGATTGCCCCACAATATGCTGGAGTCCTACATG