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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTATCAATATCTCAATCTTGTTGAAGATATTATAAGGTTCGGTGCTCAGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAGgtatttctccttaactttgagtattgaatttgatcaaccaggaaaaataatgtcattcattttcttattag

Basic information

species Zea mays
transcript GRMZM2G139880_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139880_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 5'ss of exon 3
GGAGTATCAATATCTCAATCTTGTTGAAGATATTATAAGGTTCGGTGCTCAGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAGgtattt-ctccttaacttt--gagtattgaatttgatcaaccaggaaaaataatgtcattcattttc-ttattag--------------------------------
||||||||| ||||||||||||||||||||||||||||||   |||||||||||||||||||| |||||||| || ||||| || |||||||| |||||||||||| ||| ||||  ||  || || | |||||||  |||||| || ||   |||| || | ||   | |  ||                                
GGAGTATCACTATCTCAATCTTGTTGAAGATATTATAAGGAGTGGTGCTCAGAAAAATGACAGAACAGGAACAGGGACATTATCGAAATTTGGTTGTCAGgtattttctctttaatgttgtgaataattaatttgaataaccagaaataacc-tgtctttaacttgaataaacagaaaatataacatgtctttcttttgctcatcag
















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|32838087|gb|CD977765.1|CD977765
EST:     AGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAG                         ATGCGATTCAACTTAAGGAAAAATTTTCCTCTGCTGACAACAAAG
genomic: AGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAGgtatttctcc ... ttcttattagATGCGATTCAACTTAAGGAAAAATTTTCCTCTGCTGACAACAAAG
EST: gi|67012996|gb|CO441745.1|CO441745
EST:     AGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAG                         ATGCGATTCAACTTAAGGAAAAATTTTCCTCTGCTGACAACAAAG
genomic: AGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAGgtatttctcc ... ttcttattagATGCGATTCAACTTAAGGAAAAATTTTCCTCTGCTGACAACAAAG

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), 48 (downstream exon)
Score: 100

GGAGTATCAATATCTCAATCTTGTTGAAGATATTATAAGGTTCGGTGCTCAGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAGgtatttctcc ... ttcttattagATGCGATTCAACTTAAGGAAAAATTTTCCTCTGCTGACAACAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 60

GGAGTATCAATATCTCAATCTTGTTGAAGATATTATAAGGTTCGGTGCTCAGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAGgtatttctcc ... ttcttattagATGCGATTCAACTTAAGGAAAAATTTTCCTCTGCTGACAACAAAG


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

GGAGTATCAATATCTCAATCTTGTTGAAGATATTATAAGGTTCGGTGCTCAGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAGgtatttctcc ... ttcttattagATGCGATTCAACTTAAGGAAAAATTTTCCTCTGCTGACAACAAAG


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

GGAGTATCAATATCTCAATCTTGTTGAAGATATTATAAGGTTCGGTGCTCAGAAAAATGACAGGACAGGAACTGGAACATTGTCAAAATTTGGGTGTCAGgtatttctcc ... ttcttattagATGCGATTCAACTTAAGGAAAAATTTTCCTCTGCTGACAACAAAG