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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgttcttgatcatttgccttttttatcagaactcattgagcaccgtccatgtcctgattttatttttgttcatttattctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG

Basic information

species Zea mays
transcript GRMZM2G133885_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133885_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 3
-----------gtaactgt-tcttgatcatttgccttttttatcagaactcattgagcaccgtccatgtcctgattttatttttgttcatttattctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG
           ||||     | ||   | |||  |||   | |  | |||||  || || | |||| ||  | |   | || |    || |  ||||||||||||| || ||||||||||||||||| ||||| ||||||||||| |||||||||
gttacattgaagtaatcaccttttccccctttatcttgagtgt-ggcactcacggaacatcttccaagtagtaaagctgttctc---cactgtttctgttgcagGATCCCGTTGAAACAGAACAAAGTTTTGCACGCCGTGTCTTGGCTATAGTG
















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|33285704|gb|CF075499.1|CF075499
EST:     CGTCACCCAATACTACCGTGGGCAGCATATCCATCTCCTGTCACATTGAA                         GACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG
genomic: CGTCACCCAATACTACCGTGGGCAGCATATCCATCTCCTGTCACATTGAAgtaactgttc ... tctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG
EST: gi|6194530|gb|AW146634.1|AW146634
EST:     ATATCCATCTCCTGTCACATTGAA                         GACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG
genomic: ATATCCATCTCCTGTCACATTGAAgtaactgttc ... tctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG

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), 41 (downstream exon)
Score: 154

GACTTGGAGGAACACTCTGAGGACCTTCGTCTGTTGGACCCATCGTCACCCAATACTACCGTGGGCAGCATATCCATCTCCTGTCACATTGAAgtaactgttc ... tctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

GACTTGGAGGAACACTCTGAGGACCTTCGTCTGTTGGACCCATCGTCACCCAATACTACCGTGGGCAGCATATCCATCTCCTGTCACATTGAAgtaactgttc ... tctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 187

GACTTGGAGGAACACTCTGAGGACCTTCGTCTGTTGGACCCATCGTCACCCAATACTACCGTGGGCAGCATATCCATCTCCTGTCACATTGAAgtaactgttc ... tctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 149

GACTTGGAGGAACACTCTGAGGACCTTCGTCTGTTGGACCCATCGTCACCCAATACTACCGTGGGCAGCATATCCATCTCCTGTCACATTGAAgtaactgttc ... tctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattgagcaccgtccatgtcctgattttatttttgttcatttattctgttgcagGACCCTGTTGAAACAGAACAAAGCTTTGCCCGCCGTGTCTTAGCTATAGTG
                   tcctgat  putative branch site (score: 149)
                                        tttattct  putative PPT
                        attttatttttgttca  TA-rich tract