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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatactagtgtctctatgtttttttgtcccaaaaaagccagatgattctataatttaaataatgtatccctatgttccttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCTTTCTGACTTCGGTTTGTGTAAACCTTTGGACAGCAGTAATTTCCCTAAT

Basic information

species Zea mays
transcript GRMZM2G375904_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g43570.3 (Oryza sativa), 3'ss of exon 5
gtaccatactagtgtctctatgtttttttgtcccaaaaaagccagatgattctataatttaaataatgtatccctatgttccttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCTTTCTGACTTCGGTTTGTGTAAACCTTTGGACAGCAGTAATTTCCCTAAT
||| || |  |||||  | | |||||  |      || ||    |||||||| |          ||  || || |    |  |||| ||||||||||||||||||| ||||| |||||||||| |||||||||| |||||||||||||||| || ||||||||||||||||| ||||||||||| || |||
gtatcaaataagtgttcccaagttttggt------aagaaatttgatgattcca----------aagataaccttggtgtttttttttcagGGATATCAAACCAGACAATCTATTGTTAGATCGCAGTGGTCACTTGAAGCTTTCTGACTTTGGATTGTGTAAACCTTTGGATAGCAGTAATTTTCCAAAT
















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|213171755|gb|FM196253.1|FM196253
EST:     GAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCG                         GGATATCAAACCAGATAATCTTTTGTTAGATCGCAGTGGTCACCTGAAGCT
genomic: GAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCGgtaccatact ... cttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCT
EST: gi|211127917|gb|FL461340.1|FL461340
EST:     GAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCG                         GGATATCAAACCAGATAATCTTTTGTTAGATCGCAGTGGTCACCTGAAGTT
genomic: GAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCGgtaccatact ... cttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCT
EST: gi|67018726|gb|CO447475.1|CO447475
EST:     GAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCG                         GGATATCAAACCAGATAATCTTTTGTTAGATCGCAGTGGTCACCTGAAGCT
genomic: GAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCGgtaccatact ... cttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCT

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), 49 (downstream exon)
Score: 167

TTATGCGCAAAGACACACTAACAGAAGATGAAGCTAGATTTTATATTGCAGAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCGgtaccatact ... cttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCTTTCTGACTTCGGTTTGTGTAAACCTTTGGACAGCAGTAATTTCCCTAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

TTATGCGCAAAGACACACTAACAGAAGATGAAGCTAGATTTTATATTGCAGAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCGgtaccatact ... cttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCTTTCTGACTTCGGTTTGTGTAAACCTTTGGACAGCAGTAATTTCCCTAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

TTATGCGCAAAGACACACTAACAGAAGATGAAGCTAGATTTTATATTGCAGAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCGgtaccatact ... cttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCTTTCTGACTTCGGTTTGTGTAAACCTTTGGACAGCAGTAATTTCCCTAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 356

TTATGCGCAAAGACACACTAACAGAAGATGAAGCTAGATTTTATATTGCAGAAACTGTGCTTGCCATCGAGTCTATTCACAAGCACAACTATGTTCATCGgtaccatact ... cttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCTTTCTGACTTCGGTTTGTGTAAACCTTTGGACAGCAGTAATTTCCCTAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagccagatgattctataatttaaataatgtatccctatgttccttttgtcagGGATATCAAACCAGATAATCTTTTGTTAGATCACAGTGGTCACCTGAAGCTTTCTGACTTCGGTTTGTGTAAACCTTTGGACAGCAGTAATTTCCCTAAT
                                  tccctatgttcctttt  CT-rich tract
       agatgattctataatt  TA-rich tract