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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGAAAGGGTACAGAAATAACTCAATTAGTAGTTCTGGTGGAACCTTCACCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtttttctgtgccttgtttcagtcaatcttccttttttattgataaagacagttaaaggagatttgaaaggatgaggtatacccaacgattta...

Basic information

species Zea mays
transcript GRMZM2G014788_T01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014788_T01 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os01g19470.1 (Oryza sativa), 5'ss of exon 22
CGAGAAAGGGTACAGAAATAACTCAATTAGTAGTTCTGGTGGAACCTTCACCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtttttctgtgccttgtttcagtcaatcttccttttttattgataaagac-agttaaaggagatttgaaaggatgaggtatacccaacgattta
 ||  |||| ||||||||||| || |||||| ||||||||||||| |||| |||||  ||||||||||| |||||||||||||||||||| ||||| |||||   |   | |      |  ||  |     | | | || | | | |||||     | |   ||     |  |      || || |||  |     | |  
TGAAGAAGGCTACAGAAATAATTCTATTAGTGGTTCTGGTGGAACTTTCAGCTTTGGTAACTTATTTCCAGGAAGTTTCTATCTCCGACCTCTTCTCAAGgtctctctctctctctctctctgcgttgtatattgtgccgtgtctcttgatgtcttctaaacaatcccaacatacggacatcagatattacatgttagtg-
















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|20300237|gb|BQ163180.1|BQ163180
EST:     CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTCAATCCGTCAGCAGTAGCTATCGATCTTAATTCTGGAGAG
genomic: CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
EST: gi|211471071|gb|FL253119.1|FL253119
EST:     CTTTGACAACTTATTTCCCTGGAAGTTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTCAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
genomic: CTTTGACAACTTATTTCC-TGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
EST: gi|31361738|gb|CD446095.1|CD446095
EST:     CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTCAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
genomic: CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
EST: gi|71767170|gb|DR965107.1|DR965107
EST:     CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
genomic: CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
EST: gi|18965004|gb|BM661335.1|BM661335
EST:     CCTTTGACAACTTATTTCCTGGAAGNTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTCAATCC
genomic: CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCC
EST: gi|22490517|gb|BU050440.1|BU050440
EST:     CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTCAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
genomic: CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
EST: gi|31364326|gb|CD448681.1|CD448681
EST:     CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTCAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
genomic: CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
EST: gi|87152918|gb|DY397707.1|DY397707
EST:     CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTCAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
genomic: CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
EST: gi|67011597|gb|CO440346.1|CO440346
EST:     CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAG                         GAATATAAATTCAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG
genomic: CCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAG

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), 49 (downstream exon)
Score: 296

CGAGAAAGGGTACAGAAATAACTCAATTAGTAGTTCTGGTGGAACCTTCACCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAGTCTAGGGAGGCTGAATTTCGTGCAACCAGAGTGGCTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

CGAGAAAGGGTACAGAAATAACTCAATTAGTAGTTCTGGTGGAACCTTCACCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAGTCTAGGGAGGCTGAATTTCGTGCAACCAGAGTGGCTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

CGAGAAAGGGTACAGAAATAACTCAATTAGTAGTTCTGGTGGAACCTTCACCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAGTCTAGGGAGGCTGAATTTCGTGCAACCAGAGTGGCTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

CGAGAAAGGGTACAGAAATAACTCAATTAGTAGTTCTGGTGGAACCTTCACCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtt ... tctgctgtagGAATATAAATTTAATCCGTCAGCAGTAGCTATTGATCTTAATTCTGGAGAGTCTAGGGAGGCTGAATTTCGTGCAACCAGAGTGGCTTACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGAAAGGGTACAGAAATAACTCAATTAGTAGTTCTGGTGGAACCTTCACCTTTGACAACTTATTTCCTGGAAGTTTCTATCTCCGACCACTTCTAAAGgtgctttgtttttctgtgccttgtttcagtcaatcttccttttttattgataaagacagttaaaggagatttgaaaggatgaggtatacccaacgattta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaggaga