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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcaccaagcatcatagtacacaaattgccttttctagcaatgtgttatactttaaactgtagagctaattgctacggtcatgtgttcag

Basic information

species Zea mays
transcript GRMZM2G100484_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100484_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os09g15170.1 (Oryza sativa), 5'ss of exon 12
GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagca--ccaagcatcatagtacacaaattgccttttctagcaatgtgttatactttaaactgtagagctaattgctacggtcatgtgttcag
||||||| || ||||| |||||||||||||| ||| ||||||| || || || |||||||| |||||||| ||||||||||||||  |||| ||| | |  ||| ||||    |||| | ||  | |   ||   || || || | ||   | |  |    |  ||| |||||
GAAAATTCGGTGCACTATTTGCCTCCATTCCATTCCCAATATTTGCGGCTATATACTGCGTAATGTTTGGCATTGTCGgtaagcagcccaaacat-acatgaca-aaatgattttttttcgctttttaa-atgtatttaa-tggacagtacactcattttattgtgtcttcag
















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|89763225|gb|DY690516.1|DY690516
EST:     AATATTGGCTTCCATTTACTGCGTTATGTTTGGAATTGTCG                         CTGCTGGGGGGCTGTCCTTTATGCAGTTCACCAACATGAACTCGGTGCGCA
genomic: AATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA
EST: gi|50334184|gb|CO529310.1|CO529310
EST:     TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG                         CTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA
genomic: TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA
EST: gi|60398289|gb|DN231105.1|DN231105
EST:     TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG                         CTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA
genomic: TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA
EST: gi|50334185|gb|CO529311.1|CO529311
EST:     TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG                         CTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA
genomic: TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA
EST: gi|22545627|gb|BU097986.1|BU097986
EST:     TCCTTTCACAATATTCGCTGCCATTTACTGCGGTATGCTTGGAATTGTCG                         CTGCTGGGGGGCTCTCCTTTATGC
genomic: TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGC
EST: gi|26457048|gb|CA828631.1|CA828631
EST:     TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG                         CTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACAT
genomic: TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACAT
EST: gi|211271038|gb|FL034395.1|FL034395
EST:     TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCG                         CTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA
genomic: TCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCA

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: 49 (upstream exon), 46 (downstream exon)
Score: 83

GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCAATCTCTTCATCATCGGTGTCTCACTCTTCCTGGGTTTATCTATACCAGA


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 10

GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCAATCTCTTCATCATCGGTGTCTCACTCTTCCTGGGTTTATCTATACCAGA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 13

GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCAATCTCTTCATCATCGGTGTCTCACTCTTCCTGGGTTTATCTATACCAGA


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 17

GAAAATTTGGAGCACTTTTTGCCTCCATTCCTTTCACAATATTCGCTGCCATTTACTGCGTTATGTTTGGAATTGTCGgtaagcacca ... atgtgttcagCTGCTGTGGGGCTCTCCTTTATGCAGTTCACCAACATGAACTCGATGCGCAATCTCTTCATCATCGGTGTCTCACTCTTCCTGGGTTTATCTATACCAGA