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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttgtgaacttgcctatattccacagtattgtatggttctcacttgttaccatgtagcatatatgcaactagccagtggtggaatctgttgttagccctcaattactacctgtttaagtagtctccacatctgtggtcttcattcagccctttcttctgatataaattgtttttaccatcttctccccagACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG

Basic information

species Zea mays
transcript GRMZM2G096106_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096106_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g42180.1 (Oryza sativa), 3'ss of exon 5
gtaagttttgtgaacttgcctatattccacagtattgtatggttctcacttgttaccatgtagcatatatgcaactagccagtggtggaatctgttgttagccctcaattactacctgtttaagtagtctccacatctgtggtcttcattcagccctttcttctgatataaattgtttttaccatcttctccccagACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG
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------------------------------------------------------------------------------------gtacattctgtcatt----ctccatt-ccacgtatatatatgctttttaattatcatatatgtgcataatttccatttttcgtatgtgatttttttttcgtattgttctcagACCCTTGATGTAGTTTTGCAAGTCCTCATCTCATTTCCTAATGTGAAGCCCCTGCGATCTAAG
















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|160481294|gb|EY254246.1|EY254246
EST:     AGCGTCTTGTGATGGTAAATAGGCCAGCTATTGGGATCATGTTTAAGAAA                         ACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCT
genomic: AGCGTCTTGTGATGGTAAATAGGCCAGCTATTGGGATCATGTTTAAGAAAgtaagttttg ... ttctccccagACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCT
EST: gi|89754581|gb|DY685311.1|DY685311
EST:     GCGTCTTGTGATGGTAAATAGGCCCAGCTATTGGGATCATGTTTAAGAAA                         ACCCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACC
genomic: GCGTCTTGTGATGGTAAATAGGCC-AGCTATTGGGATCATGTTTAAGAAAgtaagttttg ... ttctccccagACCC-TTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACC

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: 37 (upstream exon), 49 (downstream exon)
Score: 17

GGCTTCAATGAGCGTCTTGTGATGGTAAATAGGCCAGCTATTGGGATCATGTTTAAGAAAgtaagttttg ... ttctccccagACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG


Block sizes: 10 (upstream exon), 45 (downstream exon)
Score: 6

GGCTTCAATGAGCGTCTTGTGATGGTAAATAGGCCAGCTATTGGGATCATGTTTAAGAAAgtaagttttg ... ttctccccagACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 13

GGCTTCAATGAGCGTCTTGTGATGGTAAATAGGCCAGCTATTGGGATCATGTTTAAGAAAgtaagttttg ... ttctccccagACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 31

GGCTTCAATGAGCGTCTTGTGATGGTAAATAGGCCAGCTATTGGGATCATGTTTAAGAAAgtaagttttg ... ttctccccagACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttcattcagccctttcttctgatataaattgtttttaccatcttctccccagACCCTTGATGTAGTTTTGCAAGTCCTTGTTTCATTTCCTAGCGTGAGACCTCTGCGATCTAAG
                   ttctgat  putative branch site (score: 31)
                               ttgtttttaccatctt  putative PPT
                   ttctgatataaattgt  TA-rich tract