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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtactttatgtccgtcattcattatcactgcatgttgaagcttgtattgaccattaaacaattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTTAGAAACAATCCACAG

Basic information

species Zea mays
transcript GRMZM2G143462_T06
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 7
--gtgtactttatgtccgtcattcattatcactgcatgttgaagcttgtattgaccattaaacaattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTTAGAAACAATCCACAG
   | ||   ||| |  || |||||||| ||  || |  |   || |||||| | || |  | |||| ||||||| | | | |||| |||||||||||||||||||||| ||||||| || |||||| | || | ||||
gtttatatgctatcttggttattcattaccatcgcctactattgcatgtatttaacaattga-aatttagcagGGCGATGCAAATGATGGAGGTGGTGCTGGTGGTGGAACACTTGAGTTCCTTAGACATAACCAACAG
















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|9731839|gb|BE510591.1|BE510591
EST:     CTCCACTAGATCTTTTCCCGCAG                         GGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
genomic: CTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     CTGGTCTCTCTGGGATTCCAA-CACCGCTCCACTAGATCTTTTCCCGCAG                         C
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcag-
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     CTGGTCTCTCTGGGATTCCAA-CACCGCTCCACTAGATCTTTTCCCGCAG                         C
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcag-
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     CTGGTCTCTCTGGGATTCCAA-CACCGCTCCACTAGATCTTTTCCCGCAG                         C
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcag-
EST: gi|71764241|gb|DR962178.1|DR962178
EST:     CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAG                         GGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
EST: gi|32936801|gb|CF041620.1|CF041620
EST:     CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAG                         GGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
EST: gi|211488314|gb|FK957004.1|FK957004
EST:     CTGGTCTCTCTGGGATCCCAA-CACCGCTCCACTAGAT-TTTTCC-GCAA                         GGGGCT-CCAATGCTGAAGGTGGTGCTGGTGGGGGACCACT-GATTT-CTT
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
EST: gi|19272554|gb|BM888810.1|BM888810
EST:     CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAG                         GGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
EST: gi|211394219|gb|FL229513.1|FL229513
EST:     CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAG                         GGGGCTTC-AATGCTGGAAGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
EST: gi|22489727|gb|BU049650.1|BU049650
EST:     CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAG                         GGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
EST: gi|2615440|gb|AA661449.1|AA661449
EST:     CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAG                         GGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCAC
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCAC
EST: gi|19822693|gb|BQ048717.1|BQ048717
EST:     CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAG                         GGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
genomic: CTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
EST: gi|19351385|gb|BM895917.1|BM895917
EST:     CGCTCCACTAGATCTTTTCCCGCAG                         GGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT
genomic: CGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 171

AATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTTAGAAACAATCCACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 73

AATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTTAGAAACAATCCACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 71

AATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTTAGAAACAATCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

AATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTCCAAACACCGCTCCACTAGATCTTTTCCCGCAGgtgtacttta ... aattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTTAGAAACAATCCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcattatcactgcatgttgaagcttgtattgaccattaaacaattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTTAGAAACAATCCACAG
                              tattgac  putative branch site (score: 90)
                                      attaaacaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtactttatgtccgtcattcattatcactgcatgttgaagcttgtattgaccattaaacaattcagcagGGGGCTTCCAATGCTGGAGGTGGTGCTGGTGGTGGACCACTTGATTTTCTTAGAAACAATCCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA