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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGAAATATCTGAAGGTTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattcagaaagtagttgtttacatccttgaattcaacattgttctgaaggggcagagattgcgtgtatatttgtatatattggaccaaaggaaata...

Basic information

species Zea mays
transcript GRMZM2G067546_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067546_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g21720.1 (Oryza sativa), 5'ss of exon 9
AACGAAATATCTGAAGGTTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatc--------attcagaaagtagttgtttacatccttgaattcaacattgttctgaaggggcagagattgcgtgtatatttgtatatattggaccaaaggaaata
|| ||| |||||||||| || |||||||||   ||||||||||||||||||  ||||||||||||||||||          ||  |||  |  |   ||  | || ||| |  |||| | |||| ||   ||| | ||||  | |  |||  || |  ||||   |         
AATGAAGTATCTGAAGGCTGCAAATGTCCACCAGGTTTCAAGGGTGATGGAATAAAAAGTTGTGAAGgtattttataattgttgtgaagcttatgtattttaaccatgagtggaacacttttctaaacaagcatatattgaattttgattctta-actttgggttagc-------
















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|74242229|gb|DT650143.1|DT650143
EST:     TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAG                         ACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
genomic: TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
EST: gi|67015635|gb|CO444384.1|CO444384
EST:     TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAG                         ACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
genomic: TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
EST: gi|6227124|gb|AW155653.1|AW155653
EST:     AAAAGTTGTGAAG                         ACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
genomic: AAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
EST: gi|60396640|gb|DN229508.1|DN229508
EST:     TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAG                         ACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
genomic: TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
EST: gi|33100298|gb|CF060258.1|CF060258
EST:     TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAG                         ACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
genomic: TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
EST: gi|67019769|gb|CO448518.1|CO448518
EST:     TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAG                         ACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
genomic: TTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
EST: gi|211348715|gb|FL063226.1|FL063226
EST:     AAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAG                         ACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
genomic: AAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
EST: gi|149099685|gb|EE185734.2|EE185734
EST:     AATGGGTTTCAAGGGGGATGGAGAAAAAAGTTGTGAAG                         ACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT
genomic: AATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCT

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: 46 (upstream exon), 48 (downstream exon)
Score: 119

AACGAAATATCTGAAGGTTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCTGCAAGAATACGTGGGGAAGCTATGAATGCAGCTGTGGTGATGACAATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 875

AACGAAATATCTGAAGGTTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCTGCAAGAATACGTGGGGAAGCTATGAATGCAGCTGTGGTGATGACAATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 912

AACGAAATATCTGAAGGTTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCTGCAAGAATACGTGGGGAAGCTATGAATGCAGCTGTGGTGATGACAATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 535

AACGAAATATCTGAAGGTTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattca ... ttatttgcagACATTGATGAATGCCAAGAGAAACTTTATTGTCAGTGCAAGGGTTGCAGCTGCAAGAATACGTGGGGAAGCTATGAATGCAGCTGTGGTGATGACAATAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGAAATATCTGAAGGTTGTAAATGTCCAATGGGTTTCAAGGGTGATGGAGAAAAAAGTTGTGAAGgtatcattcagaaagtagttgtttacatccttgaattcaacattgttctgaaggggcagagattgcgtgtatatttgtatatattggaccaaaggaaata

- - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaggaaa