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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggccattagtatcgtggtcagttttagttgttctctttgtgtcgactttgagattcgctattctatactgttgctcattaacaattttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTCTTAACTCACTACAATAGGCCAATATTCAAAGTTGAGCGCCAACATACTG

Basic information

species Zea mays
transcript GRMZM2G107101_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------gtgaggccattagtatcgtggtcagttttagttgttctctttgtgtcgactttgagattcgctattcta-tactgttgctcattaa----caattttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTCTTAACTCACTACAATAGGCCAATATTCAAAGTTGAGCGCCAACATACTG
                                                        |  | |   ||      |  ||   ||| | |  || | | |     |   |    ||    |||   | |||| |||||||| ||    ||| ||| |   ||| |||||||||| ||||||||||||||||||||||||||||||||||| ||  ||||||||||||| |||||||| ||||||||||| | |||||||| ||
gtaaggcccctactctaatggttagttccaatttattggttcatttctctgtgtttgataagattttgcctctgctgtgcatttcaat-attatatctaaactgtgctgcttatagcttatcaaactactcttgctcataaagatgcaacttttat-gcagAAAGAGTACTCGGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGAGTTCTAACTCACTACAACAGGCCAATCTTCAAAGTTGATCACCAACATAGTG
















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|89106449|gb|DY576666.1|DY576666
EST:     CCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAG                         CAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTC
genomic: CCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAGgtgaggccat ... ttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTC
EST: gi|149079265|gb|EE168237.2|EE168237
EST:     ATGGTCCCCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAG                         N
genomic: ATGGTCCCCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAGgtgaggccat ... ttgaccacag-
EST: gi|149079265|gb|EE168237.2|EE168237
EST:     ATGGTCCCCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAG                         N
genomic: ATGGTCCCCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAGgtgaggccat ... ttgaccacag-
EST: gi|18963998|gb|BM660749.1|BM660749
EST:     AGCCATAATTCTGAG                         CAAGAGTACTCAGAGCAG-GGGCCTTGGCCTGTGGAGAAATTCTTAGGGTC
genomic: AGCCATAATTCTGAGgtgaggccat ... ttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTC

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), 48 (downstream exon)
Score: 260

ACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCCCCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAGgtgaggccat ... ttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTCTTAACTCACTACAATAGGCCAATATTCAAAGTTGAGCGCCAACATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

ACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCCCCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAGgtgaggccat ... ttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTCTTAACTCACTACAATAGGCCAATATTCAAAGTTGAGCGCCAACATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

ACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCCCCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAGgtgaggccat ... ttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTCTTAACTCACTACAATAGGCCAATATTCAAAGTTGAGCGCCAACATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

ACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCCCCCATTCAGTTCCTTCATCTCTTTATTCAGCCATAATTCTGAGgtgaggccat ... ttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTCTTAACTCACTACAATAGGCCAATATTCAAAGTTGAGCGCCAACATACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgactttgagattcgctattctatactgttgctcattaacaattttgaccacagCAAGAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAAATTCTTAGGGTCTTAACTCACTACAATAGGCCAATATTCAAAGTTGAGCGCCAACATACTG
                                 tcattaacaatttt  TA-rich tract