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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtataagaaatttaacatgtattcataatcgatgtggcacatgccatgccagcaatatgcttagagcttagttgcagttgacaatgaactgtgtttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGC

Basic information

species Zea mays
transcript GRMZM2G458538_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 11
gtacgtataagaaatttaacatgtattcataatcgatgtggcacat-gccatgccagc--aat--atgctt-------agagcttagttgcagttgacaatgaactgtgtttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGC
|||||||||| |||    ||   |  | |||    |||||| | || |       |    |||  |  |||       | ||   |  |  | ||||||    || || | | || |||||||||||||||||| ||||| ||||||||||||||||||| |||||| || |||||||||||
gtacgtataaaaaacactac-catgattatatggcatgtggtaaattgtttctttaattgaatagacactttcagcaaaaagaaaacattgaattgacacaacaccgt-tgttttacagTGTTTATATCTGCCTACGCAACTGCACCCAGCAGTTGAGGAGTGCCTCCTTGGCTCTTTTCGC
















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|60338618|gb|DN205591.1|DN205591
EST:     AAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAAC                         TGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTT
genomic: AAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAACgtacgtataa ... tttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTT
EST: gi|86465843|gb|DY232216.1|DY232216
EST:     AAAGTTACATACAACAAGTACCATCCCTACACATCGTGGATCCCTATAAC                         TGTTTATATCTGCCTGCGCAATTGCCCCCAGCAGTTGAGGAATGCCTCTTT
genomic: AAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAACgtacgtataa ... tttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTT

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), 47 (downstream exon)
Score: 144

GTTGGCTTTCTGTGGTATGAATATATATACAAGCTAGACAAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAACgtacgtataa ... tttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 164

GTTGGCTTTCTGTGGTATGAATATATATACAAGCTAGACAAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAACgtacgtataa ... tttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 154

GTTGGCTTTCTGTGGTATGAATATATATACAAGCTAGACAAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAACgtacgtataa ... tttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 399

GTTGGCTTTCTGTGGTATGAATATATATACAAGCTAGACAAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAACgtacgtataa ... tttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagcaatatgcttagagcttagttgcagttgacaatgaactgtgtttctttcagTGTTTATATCTGCCTGCGCAATTGCACCCAGCAGTTGAGGAATGCCTCTTTAGCTCTTTTCGC
                           agttgac  putative branch site (score: 399)
                                           tgtttctttc  putative PPT
                                             tttcttt  TA-rich tract