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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaatggccaaactcccaagattcaggtttcaaggactacacactcttactgcatgcaaaactctcctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG

Basic information

species Zea mays
transcript GRMZM2G021378_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021378_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g07200.1 (Oryza sativa), 3'ss of exon 11
gtaatgaatggccaaactccc--aagattcaggtttcaaggactacacactcttactgcatgcaaaactctcctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG
|||||||||   ||| || ||  || ||  | | | |||  |||   |    ||||  | |||||     |  ||||||||||| ||||| ||| || | ||||||||||| |||||||| ||||| |||||||| || ||| | |||
gtaatgaataagcaatcttccagaaaatcgaagctccaaatactgtgc----ttac--cttgcaa-----ttgtgaatgcagATTTTCCTCGACATGTCCGTGTTGGTTGAGGCTCAAGGCGAGATCCTGGACAATATAGAGTCACAG

upper sequence: GRMZM2G021378_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ08209 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgaatggccaaactcccaagattcaggtttcaaggactacacactc-ttactgcatgcaaaactctcctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG
                                    ||  | | | | |  | | | | | ||      |  ||    ||||||||| ||||  |||| |||||||| ||||||||||| |||||||||||| |||||||||  || 
----------------------------------gtagctcgataaatttatcaatcctttcacggtgtt--tgctctcagATCTTCATGGATATGGCCGTGTTGGTAGAAGCTCAAGGAGAGATGCTGGACGACATTGAGAACCAA

upper sequence: GRMZM2G021378_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ12216 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgaatggccaaactcccaagattcaggtttcaaggactacacactc-ttactgcatgcaaaactctcctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG
                                    ||  | | | | |  | | | | | ||  | | |  ||    ||||||||| ||||  |||| |||||||| ||||||||||| |||||||||||| |||||||||  || 
----------------------------------gtagctcgataaatttatcaatcctttcacgagtgtt-tgctctcagATCTTCATGGATATGGCCGTGTTGGTAGAAGCTCAAGGAGAGATGCTGGACGACATTGAGAACCAA

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|78075707|gb|DV504141.1|DV504141
EST:     GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG                         ATCTTCCTGGACTTGGC
genomic: GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGC
EST: gi|89250950|gb|DY622736.1|DY622736
EST:     GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG                         ATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
genomic: GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
EST: gi|78109316|gb|DV527732.1|DV527732
EST:     GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG                         ATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
genomic: GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
EST: gi|76289341|gb|DV028909.1|DV028909
EST:     GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAG                         ATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
genomic: GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
EST: gi|78124413|gb|DV542797.1|DV542797
EST:     GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATTTGCAGCAG                         ATTTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
genomic: GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
EST: gi|78075706|gb|DV504140.1|DV504140
EST:     GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATTTGCAGCAG                         ATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC
genomic: GCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGAC

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

GTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 447

GTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG


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

GTACTGGACACGCTGCAGGAGATCCAGGAGCGCCATGATACTGTGAAAGAGATTGAGAGGAAGCTTCTTGATCTGCAGCAGgtaatgaatg ... ctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaggtttcaaggactacacactcttactgcatgcaaaactctcctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG
                      ctcttac  putative branch site (score: 49)
                                        ctctcct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaatggccaaactcccaagattcaggtttcaaggactacacactcttactgcatgcaaaactctcctgaatgcagATCTTCCTGGACTTGGCTGTGTTGGTTGAAGCTCAAGGTGAGATGCTGGACAACATTGAGACGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA