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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggacaacctgcctctctgttacgatgaacaagtttgtacttagttcttactgggatctggatcaaatagtgtcaactgctttctcatgttagtaacacagtgttttctcgcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGGTAAGTTTCGTAACGTCCGTTCATCTTGAGTTGGTAAACTGCCTTAGCTATGCA

Basic information

species Zea mays
transcript GRMZM2G147882_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 8
gtaggacaacctgcctctctgt-tacgatgaacaagtttgtacttagttcttactggg---atctggatcaaatagtgtc-------aactgctttctcatgttagtaacacagtgttttct-cgcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGGTAAGTTTCGTAACGTCCGTTCATCTTGAGTTGGTAAACTGCCTTAGCTATGCA
|| || ||| |   | ||      | | |        |  |  ||  |  |||   |    |||| | |   || || |        ||||| |        ||| ||  | |  | | ||| |  || ||||||||||||||||||||||||||| ||||||| ||||||||  | ||                                                       
gttggccaaaccatcccttaaagcatgttctttggagtcattgtttttctttaggagaaccatcttggtgtcattgttttttttactaactgttactgttctttattataatacggctgtctgcatacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT------------------------------------------------------
















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|32924156|gb|CF028968.1|CF028968
EST:     ATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAG                         GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG
genomic: ATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAGgtaggacaac ... gcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG
EST: gi|32924110|gb|CF028922.1|CF028922
EST:     ATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAG                         GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG
genomic: ATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAGgtaggacaac ... gcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG

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: 46 (upstream exon), 49 (downstream exon)
Score: 36

CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAGgtaggacaac ... gcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGGTAAGTTTCGTAACGTCCGTTCATCTTGAGTTGGTAAACTGCCTTAGCTATGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 824

CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAGgtaggacaac ... gcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGGTAAGTTTCGTAACGTCCGTTCATCTTGAGTTGGTAAACTGCCTTAGCTATGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 889

CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAGgtaggacaac ... gcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGGTAAGTTTCGTAACGTCCGTTCATCTTGAGTTGGTAAACTGCCTTAGCTATGCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 40

CGGATTTATCGTCAACCTTGGCGACATGCTCGAAAGGTGGAGTAACGGCGTTTTCAGgtaggacaac ... gcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGGTAAGTTTCGTAACGTCCGTTCATCTTGAGTTGGTAAACTGCCTTAGCTATGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagtgtcaactgctttctcatgttagtaacacagtgttttctcgcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGGTAAGTTTCGTAACGTCCGTTCATCTTGAGTTGGTAAACTGCCTTAGCTATGCA
                         tagtaac  putative branch site (score: 40)
                                      ttttctcgc  putative PPT
                        ttagtaa  TA-rich tract