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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctctgatcgcattgcactcatgtttagtgcatgggttcatgagctgatgttctctgaatttgtgtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTATCCAATTTTTGAGCTGGGAAAGGTCTATTATGTCTCAAAAGGATCTCTTA

Basic information

species Zea mays
transcript GRMZM2G086934_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086934_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------gtaagtgctctgatcgcattgcactcatgtttagtgcatgggttcatgagctgatgttctctgaatttgtgtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTATCCAATTTTTGAGCTGGGAAAGGTCTATTATGTCTCAAAAGGATCTCTTA
                                       |||| |||  |    |       || |  | | ||   | | || ||||| | || || | || || ||||||    |||||||||||||||||||| |||||||| ||||||||||| |||||||||||||| || ||||||||||| ||||| || ||  |||| ||||||||||| |
gtaagtgcaacctaccgtgaaatgtttattccgtaggatgtaattgcagttcatgagcaattctgaattcttgtatgttgattgatgagttaattttgt-tggatctgtgta----cagGGCACCCAGATCCAGGCAACCATGTTCAACGAGGCTGCCAAGAAGTTCTATCCGATGTTTGAGCTGGGGAAGGTGTACTACATCTCCAAAGGATCTCTCA
















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|148943263|gb|EC888324.2|EC888324
EST:     TGCTCGTGGAGAAGGCTGCGTCTTNCA-CGTAGAACTTACTGATGAGGAT                         GGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
genomic: TGCTCGTGGAGAAGGCTGCGTCTT-CAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
EST: gi|50331879|gb|CO527005.1|CO527005
EST:     ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGAT                         GGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
genomic: ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
EST: gi|61118644|gb|DN559605.1|DN559605
EST:     ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAGCTTACTGATGAGGAT                         GGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
genomic: ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
EST: gi|78081808|gb|DV510220.1|DV510220
EST:     ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGAT                         GGCACCCAGATCCAGGCCACCATGTTTTACGAGGCTG
genomic: ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTG
EST: gi|5566971|gb|AI881882.1|AI881882
EST:     ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGAT                         GGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
genomic: ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
EST: gi|61118643|gb|DN559604.1|DN559604
EST:     ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAGCTTACTGATGAGGAT                         GGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
genomic: ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTAT
EST: gi|149086433|gb|EE175976.2|EE175976
EST:     ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGAT                         GGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGC
genomic: ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGC
EST: gi|32826012|gb|CD965690.1|CD965690
EST:     ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAGCTTACTGATGAGGAT                         GGCACCCAGATC
genomic: ATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATC

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), 49 (downstream exon)
Score: 175

GGTCATTAAGGTGCGGGTCACGAGCAAAGGCAATCTCAGAACCTACAGGAATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTATCCAATTTTTGAGCTGGGAAAGGTCTATTATGTCTCAAAAGGATCTCTTA


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

GGTCATTAAGGTGCGGGTCACGAGCAAAGGCAATCTCAGAACCTACAGGAATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTATCCAATTTTTGAGCTGGGAAAGGTCTATTATGTCTCAAAAGGATCTCTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

GGTCATTAAGGTGCGGGTCACGAGCAAAGGCAATCTCAGAACCTACAGGAATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTATCCAATTTTTGAGCTGGGAAAGGTCTATTATGTCTCAAAAGGATCTCTTA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 29

GGTCATTAAGGTGCGGGTCACGAGCAAAGGCAATCTCAGAACCTACAGGAATGCTCGTGGAGAAGGCTGCGTCTTCAACGTAGAACTTACTGATGAGGATgtaagtgctc ... gtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTATCCAATTTTTGAGCTGGGAAAGGTCTATTATGTCTCAAAAGGATCTCTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtttagtgcatgggttcatgagctgatgttctctgaatttgtgtatgcacagGGCACCCAGATCCAGGCCACCATGTTTAACGAGGCTGCAAAGAAGTTCTATCCAATTTTTGAGCTGGGAAAGGTCTATTATGTCTCAAAAGGATCTCTTA
                       agctgat  putative branch site (score: 29)
                                    tgaattt  TA-rich tract