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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtgtttcttatgatactattattgtagtttctcaaacaaaaggtttatcgctcaatctgcagttcagcaatgagcaatagcgatatgttattt...

Basic information

species Zea mays
transcript GRMZM2G081812_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081812_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g38790.3 (Oryza sativa), 5'ss of exon 6
GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtgtttcttatgatactattattgtagtttctcaaacaaaaggtttatcgctcaatctgcagttca--gcaatgagcaatagcgatatgttattt
||||||||||| |||||| | || ||||||||||||||||||||||||||||||||||||| || || |||| ||  |||   |||| | |     | |   |    |     |||  || ||||||  |  |||  |   |  |  || || | |
GAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttctgatttttataattttatatctgtaatattaatgatatgtgaaaaa--aaccaagttgaagttcatggggatgctctgaactggaatattgtgt

upper sequence: GRMZM2G081812_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G34280.1 (Glycine max), 5'ss of exon 6
GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtgtttcttatgatactattattgtagtttct----caaacaaaaggtttatcgctcaatctgcagttcagcaatgagcaatagcgatatgttattt
|||||||||||  |||| |||||||| ||||||||||||||||||| |||||||||||||  |  | | | |   |    |   || | || |    | ||| | | |  ||    | |  || |   |   ||     |  |    | |  ||    
GAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGgtaagtcatactacctctttaatagatggagttgcttttgcatctaaccagatgagtaggctttatgcttcctgttttcagattccgttgtttacacatt----

upper sequence: GRMZM2G081812_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G05390.2 (Glycine max), 5'ss of exon 6
GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtgtttcttatgatactattattgtag-tttctcaaacaaaaggtttatcgctcaatctgcagttcagcaatgagcaatagcgatatgttattt-
|||||||||||  |||| |||||||| ||||||||||||||||||| |||||||||||||  |  | | | |   |    |   || | |||| ||   ||   | | |        | |    |||  |  |   ||    |  |   |||    
GAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGgtaagtcatactacctctttaatagatggagttgctttcacatctaaccagatgagtataggctttatgcttc--ctgttttcagattcagttgtttacaca

upper sequence: GRMZM2G081812_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 5'ss of exon 6
GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtgttt--cttatgatactattattgtagtttctcaaacaaaaggtttatcgctcaatctgcagttcagcaatgagcaatagcgatatgttattt---
|||||||||||| |||| || |  ||||||||||||||||||||||||||||||||||||| ||  |  ||| | ||  ||||  |  |  |    | ||      || |    |  |||| |  |  |   ||| |||  |    | |||| |||   
GAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttatgactgccttgtaatcttattcatacaactaggtatacgttgtattaaat-tttgatcttc--taaaaacatgtgcagaatt--tttgttctttcat

upper sequence: GRMZM2G081812_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0011g01240.t01 (Vitis vinifera), 5'ss of exon 6
GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtgtttcttatgatactattattgtagtttctcaaacaaaaggtttatc---gctcaatctgcag-ttcagcaatgagcaatagcgatatgttattt
|||||||||||  |||| ||    ||||| ||||||||||||||||||||||||||||||| |   |  |    || ||| |||  | |       | |    |||  |     |   ||  | ||  |    | |  | | |    ||||   |   
GAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAGgtaagttataactacttctgtaatataatt-cattcaactggatatggagttgcttccaaccagatgggtaggctttatattttgtatttttcatattcaa---

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|113704302|gb|EE681806.1|EE681806
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|91053283|gb|EB163701.1|EB163701
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|78092548|gb|DV520922.1|DV520922
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|29945732|gb|CB815791.1|CB815791
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|78103455|gb|DV521883.1|DV521883
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|32823254|gb|CD962976.1|CD962976
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|32809367|gb|CD961601.1|CD961601
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|78544622|gb|DV622120.1|DV622120
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|37375365|gb|CF624113.1|CF624113
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|78103456|gb|DV521884.1|DV521884
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|32823328|gb|CD963050.1|CD963050
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|22818962|gb|BU499052.1|BU499052
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCCG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|56382501|gb|CV985170.1|CV985170
EST:     AAAGAAGGTTGTCGCTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|78545018|gb|DV622516.1|DV622516
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|211367145|gb|FL432827.1|FL432827
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|32823027|gb|CD962736.1|CD962736
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|71305438|gb|DR788849.1|DR788849
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG
EST: gi|21331386|gb|BQ486767.1|BQ486767
EST:     AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG                         ATGAACTCTGTTGACGCAGCGATTGATCGAAGAATATCAGAAAGTCGGCTG
genomic: AAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTG

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

GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTGGCAGGACGCATGGCCCTATGAAGAATCTGGGCTTTGCTCGGTAGATTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 184

GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTGGCAGGACGCATGGCCCTATGAAGAATCTGGGCTTTGCTCGGTAGATTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 185

GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTGGCAGGACGCATGGCCCTATGAAGAATCTGGGCTTTGCTCGGTAGATTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 134

GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtg ... gtatgagcagATGAACTCTGTTGACGCAGCAATTGATCGAAGAATATCAGAAAGTCGGCTGGCAGGACGCATGGCCCTATGAAGAATCTGGGCTTTGCTCGGTAGATTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAGgtaagttgtgtttcttatgatactattattgtagtttctcaaacaaaaggtttatcgctcaatctgcagttcagcaatgagcaatagcgatatgttattt

- - AAAGAA
- -  AAGAAG