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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaatgaacctttaatggatcctgaaatcgtgatgttcttatgtttgaagcatagctaggtagatctacttacttcttgtttatatgatggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG

Basic information

species Zea mays
transcript GRMZM2G099328_T04
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099328_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 3'ss of exon 12
----------------------------------gtgaatgaacctttaat--ggatcctg-------aaatcgtgatgttcttatgtttgaagcatagctaggtagatctacttact-tcttgtttatatgatggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG
                                   |||   ||  |||  |  | ||| |        || || || |        ||  |||  |  |  |  ||   ||| | ||| || |  | |  || | || |  ||||||||||||||| || ||||| |||||||| ||||||||||| ||||| ||||| ||||
gtacattgtataagttttagtttttcctttagtactgaccaaagtttttgttagaatctttcataatcaactcatgttacatcagagtccgaaaaaacggaacataccactaatcactgtcgttataacgtgcttgtcatgcagATTACAAACTGGCTCAATTCTCGCCCATGAAATGATGCATGCTTATCTACGTCTGAAAG
















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|14203375|gb|BG837052.1|BG837052
EST:     TCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAG                         ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
genomic: TCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
EST: gi|32859029|gb|CD998710.1|CD998710
EST:     TCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAG                         ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
genomic: TCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
EST: gi|44900705|gb|CK827250.1|CK827250
EST:     TCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAG                         ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
genomic: TCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
EST: gi|71773668|gb|DR971565.1|DR971565
EST:     CTGCAATCCTTATATTATATGGTCTGCCAAG                         ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTTG
genomic: CTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
EST: gi|76910058|gb|DV163680.1|DV163680
EST:     GACTGCAATCCTTATATTATATGGTCTGCCAAG                         ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
genomic: GACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
EST: gi|31362847|gb|CD447204.1|CD447204
EST:     TCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAG                         ATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG
genomic: TCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCG

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), 48 (downstream exon)
Score: 50

TTGGACCAGGAAACAGAATCTTAGATATGATTATAGGACCATACAAGCTGTCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 301

TTGGACCAGGAAACAGAATCTTAGATATGATTATAGGACCATACAAGCTGTCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

TTGGACCAGGAAACAGAATCTTAGATATGATTATAGGACCATACAAGCTGTCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 299

TTGGACCAGGAAACAGAATCTTAGATATGATTATAGGACCATACAAGCTGTCTCGGCGGTGTGAAGTGACTGCAATCCTTATATTATATGGTCTGCCAAGgtaaattatt ... ggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagcatagctaggtagatctacttacttcttgtttatatgatggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG
                      tacttac  putative branch site (score: 299)
                                ttgtttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatgaacctttaatggatcctgaaatcgtgatgttcttatgtttgaagcatagctaggtagatctacttacttcttgtttatatgatggttacacagATTACAAACTGGTTCCATTCTTGCCCATGAGATGATGCATGCATATCTTCGTCTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG