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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagataaagatatcatgctaacatcttttgtcaagctactgcgaaaacataccaatgcaaggtctaatttaagtaattgtcacatgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTCACCAAGGGCCAGATTCCACCAAAG

Basic information

species Zea mays
transcript GRMZM5G858094_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G858094_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 16
gtaagataaag-atatcat--gctaacatcttttgtcaagctactgcg-aaaacat-accaatgcaaggtctaatttaagt--aattgtcac-atgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTCACCAAGGGCCAGATTCCACCAAAG
|||||| |||  ||  ||     || ||| || ||| |||| | |||| ||||||| | ||||     |||| |||||| |  | || |     |||| ||||||||||||||  ||||  | |||||||||||||| |||||| ||||||| ||||||||||||||||||||||||
gtaagacaaactatgccactcattagcat-ttatgtgaagcaaatgcggaaaacatgatcaatatgtcgtcttatttaaatttatttatttttgtgctgcagAAAACAGTAACTGCCAACACGGCCACTGTTTCTGATTATGTTGGTTATCTTACCAAGGGCCAGATTCCACCAAAG
















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|32932926|gb|CF037738.1|CF037738
EST:     AAGCTGAGAGGCCCCCATGGTATATTTCAGTGGTTGGAGGTGCTTTATAT                         AAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCCC
genomic: AAGCTGAGAGGCCCCCATGGTATATTTCAGTGGTTGGGGGTGCTTTATATgtaagataaa ... catgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTC
EST: gi|32933506|gb|CF038318.1|CF038318
EST:     AAGCTGAGAGGCCCCCATGGTATATTTCAGTGGTTGGAGGTGCTTTATAT                         AAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCCC
genomic: AAGCTGAGAGGCCCCCATGGTATATTTCAGTGGTTGGGGGTGCTTTATATgtaagataaa ... catgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTC

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), 49 (downstream exon)
Score: 170

AAACAAGATTCATACTGGTTGGCTCGACACCAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATTTCAGTGGTTGGGGGTGCTTTATATgtaagataaa ... catgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTCACCAAGGGCCAGATTCCACCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 136

AAACAAGATTCATACTGGTTGGCTCGACACCAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATTTCAGTGGTTGGGGGTGCTTTATATgtaagataaa ... catgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTCACCAAGGGCCAGATTCCACCAAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 55

AAACAAGATTCATACTGGTTGGCTCGACACCAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATTTCAGTGGTTGGGGGTGCTTTATATgtaagataaa ... catgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTCACCAAGGGCCAGATTCCACCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 243

AAACAAGATTCATACTGGTTGGCTCGACACCAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATTTCAGTGGTTGGGGGTGCTTTATATgtaagataaa ... catgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTCACCAAGGGCCAGATTCCACCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgcgaaaacataccaatgcaaggtctaatttaagtaattgtcacatgctacagAAAACAGTAACCACCAATGCAGCCACTGTTTCTGAATATGTTAGTTATCTCACCAAGGGCCAGATTCCACCAAAG
                        gtctaat  putative branch site (score: 243)
                         tctaatttaagtaatt  TA-rich tract