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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaatactgtaaggtgccgtttggttcacatattggtaacgtaatgggtaatcaataagtcaataacgttacatcatgtttatttaagtccaac...

Basic information

species Zea mays
transcript GRMZM5G825902_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825902_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 5'ss of exon 6
GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaatactgtaaggtgccgtttggttcacatattggtaacgtaatgggtaatcaataagtcaataacgttaca-tcatgt---ttatttaagtccaac
|||||||||||||| ||||||||||||||||||||||| |||||| |||||||||||||||  ||| ||    || | | |  | ||  | |     |      | |   ||  ||   |  |  |    ||  ||| | |  |||   ||  | || |  |||
GAATCAAGTGAGAATTTAGCCATGGGTGAATTTTTTGGAATAAAAGCTCCTGAGAAGAAGgtgagttca---ttggatgttctcattctgcttgttcaccacccatgctctgt-tatcaagcatcttctcaattttaaagttgtgtgttttcctcaattttaac
















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|211056798|gb|FL037810.1|FL037810
EST:     AATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|60394392|gb|DN227262.1|DN227262
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|213192723|gb|FM191866.1|FM191866
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|71762075|gb|DR960012.1|DR960012
EST:     AGAAGTTAGGCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|67035504|gb|CO464037.1|CO464037
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|31355619|gb|CD439976.1|CD439976
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|24934311|gb|CA452529.1|CA452529
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|31356321|gb|CD440678.1|CD440678
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGGTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|31353042|gb|CD437399.1|CD437399
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|211133671|gb|FL369481.1|FL369481
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAN                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACC
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACC
EST: gi|194716957|gb|FK934116.1|FK934116
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTCGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|60394317|gb|DN227187.1|DN227187
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|31360452|gb|CD444809.1|CD444809
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|149100918|gb|EE187014.2|EE187014
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|8516597|gb|BE123322.1|BE123322
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|5847192|gb|AW000271.1|AW000271
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|5325091|gb|AI783282.1|AI783282
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|149074677|gb|EE163095.2|EE163095
EST:     AAGTTAGCCATGGGGGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|32828950|gb|CD968628.1|CD968628
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|149074678|gb|EE163096.2|EE163096
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGAC
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGAC
EST: gi|71447368|gb|DR828418.1|DR828418
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|32828741|gb|CD968419.1|CD968419
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|148999647|gb|EE036634.2|EE036634
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|6194493|gb|AW146597.1|AW146597
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|31363719|gb|CD448076.1|CD448076
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|5871295|gb|AW017766.1|AW017766
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|5860476|gb|AW011698.1|AW011698
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|5871459|gb|AW017930.1|AW017930
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA

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: 229

GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 498

GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 621

GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaatactgtaaggtgccgtttggttcacatattggtaacgtaatgggtaatcaataagtcaataacgttacatcatgtttatttaagtccaac

- - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG