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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatgttccaaactatgttgcttttctggttgctggtttggtcaattgcttttggaggtaactcaacttgctatttggttattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG

Basic information

species Zea mays
transcript GRMZM2G153977_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153977_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 8
gtttgtatgttccaaactatgttgcttttctggttgctggtttggtcaattgcttttggaggtaactcaacttgctatttgg--ttattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG
         ||  ||  |   |   ||||||||   | | ||| |||||||   | |      || | ||    || | |||  |||| |||||||| || ||| | || ||||| ||||||||||| ||||| ||||||||||| |  || ||||||||
-------gtttgtaatttgcttcaattttctggaaacagcttttgtcaattatatctttgatgaattaaaacaactttctgggattatgttgcagACACAGCCATCAAAAATCTGCTCTCAGGTTGGTCTGTGTACTTTTGATGGGAAGCATGGTGTTAG
















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|60344077|gb|DN211050.1|DN211050
EST:     GACAACAGATCCTAGATCTTCTGCTAGCTGAG                         ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
genomic: GACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
EST: gi|60400185|gb|DN232992.1|DN232992
EST:     CTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAG                         ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
EST: gi|21331514|gb|BQ486895.1|BQ486895
EST:     CTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAG                         ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
EST: gi|78120564|gb|DV538948.1|DV538948
EST:     TCCTAGATCTTCTGCTAGCTGAG                         ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
genomic: TCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
EST: gi|31627888|gb|CD526338.1|CD526338
EST:     CTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAG                         ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
EST: gi|67015196|gb|CO443945.1|CO443945
EST:     CTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAG                         ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC
genomic: CTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGC

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: 361

AATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 601

AATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 657

AATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 813

AATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATCTTCTGCTAGCTGAGgtttgtatgt ... tattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttggtcaattgcttttggaggtaactcaacttgctatttggttattttgcagACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG
                     aggtaac  putative branch site (score: 813)
                                            ttatttt  putative PPT
                                     tatttggttatttt  TA-rich tract