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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattcgctcatatgataaaatgttgtatgaatggtatgatgcttatgctggccttattgatatgatctttttgttgcttattttaattcaccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGATGAATCAAGTTTGACAGGTGAACCTATGCCTGTAACAAAGATAACAGGG

Basic information

species Zea mays
transcript GRMZM2G315931_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315931_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 3'ss of exon 6
----aaaattcgctcatatgataaaatgttgtatgaatggtatgatgcttatgctggccttattgatatgatctttttgttgcttattttaattcaccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGATGAATCAAGTTTGACAGGTGAACCTATGCCTGTAACAAAGATAACAGGG
     ||| | | | ||||||| ||||    ||||  | |  |  ||  |   |      |||   ||   | |     ||||||| |   || | |  |  ||||||   | |||||||||||| |||| ||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
attataaacttgtt-atatgatgaaatccattatggttagcttt-tgtatggtcctatgctatgcttagagtgtaaccattgcttaat--gatgcgctgtctagGATCGTGTTCCAGCAGACGGTGTTGTCAAATCTGGACGGAGTACAGTTGATGAATCAAGTTTGACAGGTGAACCTATGCCTGTAACAAAGATAGCAGGG
















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|211050287|gb|FL014623.1|FL014623
EST:     TCCCATGTGATACTCTAGCTGTTGGGGACTATGTTGTTGTGCTACCTGGG                         GATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGAT
genomic: TCCCATGTGATACTCTAGCTGTTGGGGACTATGTTGTTGTGCTACCTGGGgtgagtacag ... caccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGAT
EST: gi|211050286|gb|FL014622.1|FL014622
EST:     TCCCATGTGATACTCTAGCTGTTGGGGACTATGTTGTTGTGCTACCTGGG                         GATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGAT
genomic: TCCCATGTGATACTCTAGCTGTTGGGGACTATGTTGTTGTGCTACCTGGGgtgagtacag ... caccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGAT

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), 47 (downstream exon)
Score: 229

AGCACGCCTAATGGTGGATAATGATGCTGAGAAATCATCATTGATTGAAGTCCCATGTGATACTCTAGCTGTTGGGGACTATGTTGTTGTGCTACCTGGGgtgagtacag ... caccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGATGAATCAAGTTTGACAGGTGAACCTATGCCTGTAACAAAGATAACAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

AGCACGCCTAATGGTGGATAATGATGCTGAGAAATCATCATTGATTGAAGTCCCATGTGATACTCTAGCTGTTGGGGACTATGTTGTTGTGCTACCTGGGgtgagtacag ... caccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGATGAATCAAGTTTGACAGGTGAACCTATGCCTGTAACAAAGATAACAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

AGCACGCCTAATGGTGGATAATGATGCTGAGAAATCATCATTGATTGAAGTCCCATGTGATACTCTAGCTGTTGGGGACTATGTTGTTGTGCTACCTGGGgtgagtacag ... caccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGATGAATCAAGTTTGACAGGTGAACCTATGCCTGTAACAAAGATAACAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

AGCACGCCTAATGGTGGATAATGATGCTGAGAAATCATCATTGATTGAAGTCCCATGTGATACTCTAGCTGTTGGGGACTATGTTGTTGTGCTACCTGGGgtgagtacag ... caccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGATGAATCAAGTTTGACAGGTGAACCTATGCCTGTAACAAAGATAACAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctggccttattgatatgatctttttgttgcttattttaattcaccatacagGATCACATCCCAGCAGACGGTATTGTGAAAGCTGGAAGGAGTACAGTTGATGAATCAAGTTTGACAGGTGAACCTATGCCTGTAACAAAGATAACAGGG
                                     ttttaat  putative branch site (score: 223)
                        tttttgttgcttattt  TA-rich tract