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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTTGTCTTACAACCGCTTTACTGGACCAATCCCATTCAACATTGGTTTCCTACAAGTGGCTACACTgtatgttctgtttgccctttttttcactgaaaatgacgtaattacatgcctaatatatacaagcttacctgcaaatatgcgtgcatcctttatcag

Basic information

species Zea mays
transcript GRMZM5G809695_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G809695_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 10
GGATTTGTCTTACAACCGCTTTACTGGACCAATCCCATTCAACATTGGTTTCCTACAAGTGGCTACACTgtatgttctgtttgccctttttttcactgaaaatgacgtaattacatgcctaatata-tacaagcttacctgcaaatatgcgtgcatccttt--atcag
|||||||||||||||     || ||||| |||| || ||||||||||||||||||||||| ||||||||||||||  || ||  |      || ||  ||||  ||  ||||| |||  ||||| | |    ||| | |||||    |     |||  |||  || ||
GGATTTGTCTTACAATAAACTTTCTGGATCAATTCCTTTCAACATTGGTTTCCTACAAGTTGCTACACTgtatgtggtgattatc------ttgacaaaaaaaaactcaattaaatgtttaatacagtttttgctgatctgcatgattattcacattgtttgaattag
















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|211377235|gb|FL413744.1|FL413744
EST:     TTTACTGGACCAATCCCATTCAACATTGGTTTCTTACAAGTGGCTACACT                         ATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGNAATTGGCCT
genomic: TTTACTGGACCAATCCCATTCAACATTGGTTTCCTACAAGTGGCTACACTgtatgttctg ... cctttatcagATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGTAATTGGCCT
EST: gi|211280748|gb|FL403182.1|FL403182
EST:     TTTACTGGACCAATCCCATTCAACATTGGTTTCTTACAAGTGGCTACACT                         ATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGTAATTGGCCT
genomic: TTTACTGGACCAATCCCATTCAACATTGGTTTCCTACAAGTGGCTACACTgtatgttctg ... cctttatcagATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGTAATTGGCCT
EST: gi|211397955|gb|FL395271.1|FL395271
EST:     TTTACTGGACCAATCCCATTCAACATTGGTTTCTTACAAGNGGCTACACT                         ATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGTAATTGGCCT
genomic: TTTACTGGACCAATCCCATTCAACATTGGTTTCCTACAAGTGGCTACACTgtatgttctg ... cctttatcagATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGTAATTGGCCT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1538

GGATTTGTCTTACAACCGCTTTACTGGACCAATCCCATTCAACATTGGTTTCCTACAAGTGGCTACACTgtatgttctg ... cctttatcagATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGTAATTGGCCTTATGCAGGCTCTCGCTGTCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

GGATTTGTCTTACAACCGCTTTACTGGACCAATCCCATTCAACATTGGTTTCCTACAAGTGGCTACACTgtatgttctg ... cctttatcagATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGTAATTGGCCTTATGCAGGCTCTCGCTGTCCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 135

GGATTTGTCTTACAACCGCTTTACTGGACCAATCCCATTCAACATTGGTTTCCTACAAGTGGCTACACTgtatgttctg ... cctttatcagATCCTTGCAAGGGAACAAGTTCACTGGCCCAATTCCTTCAGTAATTGGCCTTATGCAGGCTCTCGCTGTCCT