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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggagaagaatgttggattttttcccccagattcatacttgtgtgctaagctggcgtggaatattttgtatgcag

Basic information

species Zea mays
transcript GRMZM2G416120_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggag----aagaatgttggatttt---ttcccccagattcatacttgtgtgctaagctggcgtggaatattttgtatgcag
 |||||||| ||||| |||||||| |||||||| ||||| |||| ||| || || |||||||| ||||||||||| |||||||||||||||||||||||||| ||||||    || ||  |   ||||    ||   |    ||| |   || | || || |    |  ||  | ||  | |||||
AGGTGTTGCACTTCTTTATGCATCAAAGGAGCTGGATAAATTGCCGACTGCTAACTTTGATCAAAAGATTGGTGTACAAATCATTCAGAATGCTTTGAAGgtttgggagggataataacttctcatttcctgttttgctgatttcttctctgggagcaaaacc--tgatgacaacttattttgcag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggagaagaatgttggattttttcccccagattcatacttgtgtgctaagctggcgtggaatattttgtatgcag--------------------------------------------------------------------------------------------------------------------
||||||||||||||| ||||||||||  ||| | |||||| | || || || || |||||||| ||||| ||||| || ||||| || ||||||||||||||  | |       | |     ||||      ||||      | |  |  |     |  | | | || |    |   ||                                                                                                                    
TGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttcttttgctgattttcattttagatcttccatagcattgtttctggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagctttacttgcctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctggga-----gaagaatgttggattttttcccccagattcatacttgtgtgctaagctggcgtggaatattttgtatgcag-----------------
||||||||||||||| ||||| || || ||| | |||||  | || || || || |||||||||||||||||||| || || || || |||||||| |||||  |        |||   | |  |||||  ||    || | |        |   |  | |  | |     || ||||     |                 
TGGTGTTGCTCTTCTATATGCGTCAAAAGAGTTGGATAAACTTCAAACTGCTAACTTTGATCAGAAGATTGGTGTCCAGATTATCCAAAATGCTTTAAAGgttagttttctctgaattttttctgatttcctcttt-agctcctctaaatcgcattttgattacattacggatcttgtggaaggaaaaccagcaccagatt

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggagaagaatgttggattttttcccccagatt---catacttgtgtgctaagctgg---------cgtggaatattttgtatgcag---------
|||||||||||||||||||||||| |  ||| | |||||| | || || || || |||||||| ||||| || || || ||||| || ||||||||||||||  | |       | |     ||||      |||||   ||||    |||     |  ||         |   || | || | | |             
TGGTGTTGCTCTTCTCTATGCATCAAGTGAGTTGGATAAGCTTCAAACTGCTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttcttttgctgattttcattttagattatccatagcattgtttctggtaggtcactactccacagatttttctctctctcatcccttatt

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 14
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgt-ctgggagaagaatgttggattttttcccccagattcatacttgtgtgctaagctggcgtggaatattttgt--atgcag
||||||||||||| | ||||| ||||| || || || ||| |    ||||| || ||||||||||| |||||||| ||||||||||| || ||  | |||||  |      |  |  |||    |  || |    ||  | |  |    |         |    ||| |||  |  ||||||
TGGTGTTGCTCTTTTGTATGCTTCGAAAGAACTTGAGAAGCTTTCCACAGCTAACTTTGATCAGAAAATTGGTGTTCAAATCATTCAAAACGCACTCAAGgtgtttctctcatcacattgttcatcctcgctagcataaacagcttctagaatcttacacacaaaatctttctttgatgcag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggagaaga-atgttggattttttcccccagattcatacttgtgtgctaagctggcgtggaatattttgtatgcag--------------------
||| || || ||||| ||||| || || ||| | || ||  |||  ||| |||| |||||||||||||||||||| || || || ||||||||| |||| ||  |     |   || ||  | | |||     | |||| |     ||   ||  |||      | | || || |  ||                     
TGGCGTGGCACTTCTTTATGCTTCCAAAGAGTTGGACAAACTGCCAACATCAAACTTTGATCAGAAGATTGGTGTTCAGATTATCCAGAATGCTCTGAAAgttagtattcattcattttctaatatttaaaagacattcctcagcttggattagtctgtaaataattcttgtggaatcacacaagagtcattcaggatag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 14
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 5'ss of exon 15
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgt-----ctgggagaagaatgttggattttttcccccagattcatacttgtgtgctaagct--ggcgtgg--aatattttgtatgcag-------------------------------------------------------------------
||||||||||||  | ||||| ||   |||||| |||||| | || || || || |||||||||||| |||| ||||||||||| |||||||| ||||||||      || |  |       |||| |   |     | ||  |    | |||      ||  || | ||  | | | |||   |||                                                                    
TGGTGTTGCTCTATTGTATGCTTCCCGGGAGCTTGATAAGATTCAAACCGCGAACTTTGATCAGAAGGTTGGAGTGCAAATCATCCAGAATGCCTTGAAGgtactttttgtgcaacttgatctggagtgagtttgtaaaatgaacgaatctgtatcggacttaggagaggctattgtcttgatcgcatcagcttatgtgtcctctttactgggagtaaaatttcggtgaaatgtaatgagcatgttgtactgcag

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|6445583|gb|AW179546.1|AW179546
EST:     TTGGTGTGCGAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACGCCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: TTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|149073907|gb|EE162235.2|EE162235
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|31349659|gb|CD434016.1|CD434016
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|32914117|gb|CF018929.1|CF018929
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGGCTGGGGTGGAGGGAGCAGTAGT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAAT-GCTGGGGTGGAGGGAGCAGTAGT
EST: gi|91875568|gb|EB405525.1|EB405525
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|60337000|gb|DN203973.1|DN203973
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|60353910|gb|DN220883.1|DN220883
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|24764192|gb|CA399359.1|CA399359
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGC-TTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|78078493|gb|DV506906.1|DV506906
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|87152342|gb|DY397131.1|DY397131
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACAC
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACAC
EST: gi|67023389|gb|CO452138.1|CO452138
EST:     CGAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|60347399|gb|DN214372.1|DN214372
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|149077208|gb|EE165874.2|EE165874
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|32858330|gb|CD998011.1|CD998011
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|37374359|gb|CF623530.1|CF623530
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|4874396|gb|AI673916.1|AI673916
EST:     AGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACNCCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: AGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|30088021|gb|CB886226.1|CB886226
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|21432198|gb|BQ547688.1|BQ547688
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|28982390|gb|BQ538103.2|BQ538103
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|32857688|gb|CD997369.1|CD997369
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTANTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
EST: gi|30088022|gb|CB886227.1|CB886227
EST:     CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAG                         ACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT
genomic: CAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTT

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: 376

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTTGTGGGCAAGCTTTTGGAGCAAGGAAACACTGACCTTGGTTATGATGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 157

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTTGTGGGCAAGCTTTTGGAGCAAGGAAACACTGACCTTGGTTATGATGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 131

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTTGTGGGCAAGCTTTTGGAGCAAGGAAACACTGACCTTGGTTATGATGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 366

TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggaga ... ttgtatgcagACACCTGTACACACCATTGCCTCCAATGCTGGGGTGGAGGGAGCAGTAGTTGTGGGCAAGCTTTTGGAGCAAGGAAACACTGACCTTGGTTATGATGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtctgggagaagaatgttggattttttcccccagattcatacttgtgtgctaagctggcgtggaatattttgtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG