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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcacatcatccatttcaatttcaatttgtatttgtatttttgtgaagttcttaatacataaaatttgctagtag

Basic information

species Zea mays
transcript GRMZM2G056393_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 12
TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcacatcatccatttcaatttcaatttgtatttgtatttttgtgaagttcttaatacataaaatttgctagtag
|||||||| ||||||||||| ||||| || |||||||||||||||||||| ||| ||||| | || |||||  ||||||||    | |||  ||  | |||   | |  || | |   |||||||| ||  |||    |||| |||| | | ||
TTTTCAAAGGCTCTGAATCGTTTCCAGAAAGAGGATCCTACTTTCCGTGTAGGTCTGGATCCAGAAAGTGGAGAGgtttgttttgttatctgttgtatttt---tctaaatctat-catttgtgaactt--taaagtgtaaattttgatcgcag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA01G14800.1 (Glycine max), 5'ss of exon 7
TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcacatcatccatttcaatttcaatttgtatttgtatttttgtgaagttcttaatacataaaatttgctagtag
|||||||||||| |||||||||||||||| || |||||||| || ||||| || |||||  | |||||||| ||||||      |   |   | ||| | ||  ||         ||| ||||     |||| ||   |||  | ||    |||
TTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACATTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAGgttatctttaatttttttatcattctcttttaagtaaaacattattgtttgtatcttgattagtaatttctgtggttag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA11G16460.1 (Glycine max), 5'ss of exon 12
TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcacatcatccatttcaatttcaatttgtatttg-tatttttgtgaagttcttaatac--ataaaatttgctagtag-
|||||||||||| |||||||||||||||| || ||||||||||| ||||| || |||||  | |||||||| ||||||      |         ||| | ||  |||   |    |||| ||||     | || |||    |||| ||   | ||   
TTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAGgttatctttaattctttgatcattctctttttaagtacaatattattgttcgtatgttgatattagtaaacttctgtggttag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 5'ss of exon 12
TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgt-ttgtcacatcatccatttcaatttca--atttgtatttgtatttttgtga--agttcttaatacataaaatt-tgctagtag---------------
|| || ||||| |||||||| ||||| || |||||||||||||||||||||||||||||| | |||||||||||||| |  ||  |  |  | |||   | |||  |    | | |  |||      |  |||  |||| |   |  ||| | | | |                 
TTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAGgtatcatctaaaaactcttttgcttctcagcaccactctcttaattcaccccattagtatttaacattgaggattcttccatttatccgtaatgggacag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 5'ss of exon 12
TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgt-ttgtcacatcatccatttcaatttca--atttgtatttgtatttttgtga-agttcttaatacataaaatt-tgctagtag---------------
|| || |||||  ||||||| ||||| || |||||||||||||||||||||||||||||| | |||||||||||||| |  ||  |  |  | |||   | |||  |  | | | |  |||      | |||  |||| |   |  ||| | | | |                 
TTCTCGAAAGCATTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAGgtatcatctaaaaactcttttgcttctcagcacctctctcttaattcaccccatagtatttaacattgatgattcttccatttatccttcatgggacag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 5'ss of exon 12
TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttg--tcacatcatccatttca-atttcaatttgtatttgtatttttgtgaagttc--ttaatacataaaatttgctagtag-----
|||||||| ||| |||||||||| || |  |||||||||||||||||||| || ||||| ||||||||||| |||||||   | |   ||| ||||||| |  |   || |     | | |||| | | |       |  |||| ||| |   |  | |     
TTTTCAAAGGCTTTGAATCGCTTTCAGAGAGAGGATCCTACTTTCCGTGTTGGGTTGGACGCTGAGAGTGGGCAGgtttaatttatgacatgcatttcacacattccttagaggaagaagttttatcatgcctaaccatgacatcaaaatgctttcttgtgcag

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|32930091|gb|CF034903.1|CF034903
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCAGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|91874831|gb|EB404788.1|EB404788
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|6194594|gb|AW146698.1|AW146698
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|6020648|gb|AW065681.1|AW065681
EST:     GGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: GGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|211410070|gb|FL355701.1|FL355701
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|32801951|gb|CD954187.1|CD954187
EST:     GATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCAGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: GATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|118406757|gb|EH038205.1|EH038205
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|32788275|gb|CD940511.1|CD940511
EST:     GATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: GATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|211409847|gb|FL347405.1|FL347405
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|67017174|gb|CO445923.1|CO445923
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
EST: gi|211430479|gb|FL350077.1|FL350077
EST:     AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG                         ACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT
genomic: AAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGT

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), 39 (downstream exon)
Score: 167

TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 163

TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 202

TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 138

TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcaca ... ttgctagtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAGgtttgtcacatcatccatttcaatttcaatttgtatttgtatttttgtgaagttcttaatacataaaatttgctagtag

- - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG