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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTTTGCTGCATGGCTGTTAAACAAGAAACCAGATGGCTTGAGACGTTTAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctgttttttgttcatttaattaatcttatgaaccaaatttgcacatattttaatcctttattattggatatcaaaatcctgtttcaactagtg...

Basic information

species Zea mays
transcript GRMZM2G069676_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069676_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 5'ss of exon 4
AGCTTTTGCTGCATGGCTGTTAAACAAG---AAACCAGATGGCTTGAGACGTTTAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctgttttttgttcat---ttaattaatcttatgaaccaaatttgcacatattttaatcctttattattggatatcaaaatcctgtttcaactagtg-
    |||||||||||| | |||||||||   ||| | ||||| | ||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||| ||||||| |  | || |   || ||| | | | |   | ||||    |   |||  |  | || |  | |  |  |||    | | |    ||||    
---ATTTGCTGCATGGTTATTAAACAAGAAGAAAGCGGATGGATGGAGACGTTTAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctgttctccgctcttatttttattgaacctttattcaaaata---atgcattgcatgctttaaggaattaagctcacc-ccttataattactaaaat
















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|32851046|gb|CD990727.1|CD990727
EST:     TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAG                         AACGCAGTCACTCATGG
genomic: TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGG
EST: gi|71332327|gb|DR803103.1|DR803103
EST:     TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAG                         AATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTT
genomic: TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTT
EST: gi|76289294|gb|DV028862.1|DV028862
EST:     TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAG                         AATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTT
genomic: TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTT
EST: gi|18659547|gb|BM500395.1|BM500395
EST:     TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAG                         AATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTT
genomic: TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTT
EST: gi|101389188|gb|EB816549.1|EB816549
EST:     TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAG                         AATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTT
genomic: TAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTT

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), 46 (downstream exon)
Score: 128

AGCTTTTGCTGCATGGCTGTTAAACAAGAAACCAGATGGCTTGAGACGTTTAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTTGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 188

AGCTTTTGCTGCATGGCTGTTAAACAAGAAACCAGATGGCTTGAGACGTTTAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTTGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 194

AGCTTTTGCTGCATGGCTGTTAAACAAGAAACCAGATGGCTTGAGACGTTTAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTTGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 178

AGCTTTTGCTGCATGGCTGTTAAACAAGAAACCAGATGGCTTGAGACGTTTAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctg ... ttattgtcagAATGCAGTCACTCATGGAATCACTACTGCTGGACACGATATCCTACAGTTTGG