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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctgtaacatttcacattttcaatttggtctttctgtaacttaatttcttcttgtttccttttatcgaatatccataattctttcttgtttccttttatcgaacatccag

Basic information

species Zea mays
transcript GRMZM2G052926_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052926_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 5'ss of exon 8
GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctgtaacatttcacattttcaatttggtctttctgtaacttaatttcttcttgtttccttttatcgaatatccataattctttcttgtttccttttatcgaacatccag
|||||||||||||| || ||||||||||| ||||| |||||||||||||||||||| |  | ||   ||  | ||  |||||  |  || |      |  | | ||||||||||||| |||   |                                         
GGAAGGAACATATATGACGGTTGCTGCCAGCTAGACATTCAATATTCAAAgtatgacccatgactagtcttagttgaaatttatttatttttctcaatcttattttcttgtttccttgtatttcag----------------------------------------
















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|31361372|gb|CD445729.1|CD445729
EST:     GGAAGGAACATATACGATGGCTGCTGCCAACTAGATATTCAATATTCAAA                         TCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
genomic: GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
EST: gi|67014377|gb|CO443126.1|CO443126
EST:     GGAAGGAACATATACGATGGCTGCTGCCAACTAGATATTCAATATTCAAA                         TCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
genomic: GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
EST: gi|31358368|gb|CD442725.1|CD442725
EST:     GGAAGGAACATATACGATGGCTGCTGCCAACTAGATATTCAATATTCAAA                         TCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
genomic: GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
EST: gi|211448114|gb|FL293416.1|FL293416
EST:     CAATATTCAAA                         TCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
genomic: CAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
EST: gi|78087001|gb|DV515394.1|DV515394
EST:     GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAA                         TCTCAGTGAACTGCAAGTCCACTA
genomic: GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTA
EST: gi|61118023|gb|DN558984.1|DN558984
EST:     AAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAA                         TCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
genomic: AAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
EST: gi|78080905|gb|DV509317.1|DV509317
EST:     GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAA                         TCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
genomic: GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
EST: gi|32943654|gb|CF048473.1|CF048473
EST:     GGAAGGAACATATACGATGGCTGCTGCCAACTAGATATTCAATATTCAAA                         TCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG
genomic: GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG

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), 42 (downstream exon)
Score: 101

GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 66

GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 47

GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 78

GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctg ... gaacatccagTCTCAGTGAACTGCAAGTCCACTACAACAACGACCGATCTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGGAACATATACGATGGTTGCTGCCAACTAGATATTCAATATTCAAAgtatgagctgtaacatttcacattttcaatttggtctttctgtaacttaatttcttcttgtttccttttatcgaatatccataattctttcttgtttccttttatcgaacatccag

- AAGGAA
- - - - - - - - - -  TGCTGC