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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGATTATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaagttcatttcacaaatcgctatacatgtcatgtcgacgtctttatgtgtctttctttttgtattttcttatgataatgtcctatcttcttgaatatt...

Basic information

species Zea mays
transcript GRMZM2G154892_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154892_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g08730.1 (Oryza sativa), 5'ss of exon 12
GGGATTATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaagttcatttcacaaatcgctatacatgtcatgtcgacgtctttatgtgtctttctttttgtattttcttatgataatgtcctatcttcttgaatatt-----
|||| || ||||||||||||||||||||||| ||||||||||||||||||||||||||| |  ||||   || || | |||| |||||||||  || | |||||         ||  | | ||| |||||      ||  ||||||||  ||| ||     
GGGACTACGATTTAAAGGTCATGCGCCAGGAATACTACATTAACAGGCAAAAAACGgtatgcacattcatcacatgg-tatatatgtcatgtacacttatttattgtcagcagttcctttgtttgcttattg----gtggtatcttctataatgttatgaa

upper sequence: GRMZM2G154892_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA17G15510.1 (Glycine max), 5'ss of exon 12
GGGATTATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaagttcatttcacaaatcgctatacatgtcatgtcgacgtctttatgtgtctttctttttgtattttcttatgataatgtcctatcttcttgaatatt-
| ||||||||||| |||||||||||||| ||||||||||||||  |||| ||| | ||||||| |   |||  ||    ||     |  | |  | |  | | |     | | ||    ||| ||| |  |||  |    ||  | ||  ||  || 
GTGATTATGATTTGAAGGTCATGCGCCAAGAGTACTACATTAATCGGCAGAAAGCAgtaagtttagc-cacttatgttgattgtgattgttttaatgaatatgtcctgatgtgttggaatatgttcgttagattcttgtgtacatcctccaaattta

upper sequence: GRMZM2G154892_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv00s0333g00070.t01 (Vitis vinifera), 5'ss of exon 9
GGGATTATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaag--ttcatttcacaaatcgctatacatgtcatgtcgacgtctttatgtgtctttctttttgtattttcttatgataatgtcctatcttcttgaatatt----------------------
| ||||||||||||||||||||||| || |||||||| |||||  | || || |||||| |  |   ||    | || |  ||   ||  |  |  |     || |||  |||        ||||   | |||  ||     ||| |  |  |  |||                      
GTGATTATGATTTAAAGGTCATGCGACAAGAGTACTATATTAATCGACAGAAGACGGTAGGGATCTCTTCTTTATATTgtcatttttggaacatttataatatt-tgta-cttcagaaagatattgattaatgcaaaaactatatttattgaagaattttttcaagaatnnnnnnnnnnn

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|211185924|gb|FL329926.1|FL329926
EST:     ATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACG                         TTCATCAATCACTTGGTTAATCAGCTTGCCAGACACCAGTTTCTGAAGATT
genomic: ATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaagttcat ... cattttgcagTTCATCAATCACTTGGTTAATCAGCTTGCCAGACACCAGTTTCTGAAGATT




















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), 49 (downstream exon)
Score: 419

GGGATTATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaagttcat ... cattttgcagTTCATCAATCACTTGGTTAATCAGCTTGCCAGACACCAGTTTCTGAAGATTGCTTGCCAACTTGAAAGGAAGAATATAGCTAGTGCGTACTCATTGCTTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 141

GGGATTATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaagttcat ... cattttgcagTTCATCAATCACTTGGTTAATCAGCTTGCCAGACACCAGTTTCTGAAGATTGCTTGCCAACTTGAAAGGAAGAATATAGCTAGTGCGTACTCATTGCTTA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 103

GGGATTATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaagttcat ... cattttgcagTTCATCAATCACTTGGTTAATCAGCTTGCCAGACACCAGTTTCTGAAGATTGCTTGCCAACTTGAAAGGAAGAATATAGCTAGTGCGTACTCATTGCTTA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 337

GGGATTATGATTTAAAGGTCATGCGCCAGGAGTACTACATTAACAGGCAAAAAACGgtaagttcat ... cattttgcagTTCATCAATCACTTGGTTAATCAGCTTGCCAGACACCAGTTTCTGAAGATTGCTTGCCAACTTGAAAGGAAGAATATAGCTAGTGCGTACTCATTGCTTA