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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgtatgaacttatcttggttttgattttaatatttttccctaataagttgttataccagcag

Basic information

species Zea mays
transcript GRMZM2G165418_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 2
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgtatgaacttatcttggttttgattttaatatttttccctaat--aagttgttataccagcag
|||||| ||||||||||| ||||| ||||||||||| ||||||||||| || || | |||||||||||| |||||||||||||||||||||| |||||||||||||||||   || ||||||| |||||   |  |||| | ||||||   || ||  ||||   | |   |||||
CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcaccattagt-tgaacttctcttg--ctcaatttcattattttatactcatgaaagtctatctgttagcag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G20830.1 (Glycine max), 5'ss of exon 2
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgt-----atgaacttatcttggttttgattttaatatttttc---cctaataagttg----ttataccagcag----------------------------------
 || || ||||| |||||||||||||| |||||||| |||||||| ||||| |||   || || || || ||| | |||||| ||||||||      |||||||     |  | |     |  || || | ||     | |  ||| ||   ||      | | |  ||     ||| |||   |                                   
TATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAACGGACAGATACAAAAGATgtaattctgattttttcttcagcaatttcttttataactaaaattactaaacttaaggtttgaaagattccattttacacccttaatttctctaatatctatgtatactgtaacttgcag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 2
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgt-----atgaacttatcttggttttgattttaatattttt--ccctaataagttg---ttataccagcag---------------------------------
 || || ||||| |||||||||||||| |||||||| |||||||| ||||| |||   || || || || ||| | |||||  ||||||||      ||||||||    |  | |     |  || || | ||     | |  ||| ||  ||      |||  | |     ||| |||   |                                  
TATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGTGGTGGTCGAGTAGTTCTCTTTGAGCGGACAGATACAAAAGATgtaagtctaattttttcttcagcaatttcttttataactaaaattactaacttaggttttaaagattctactttacacccttaattttctaatatctatgtatactgtaacttgcag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 2
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgtatgaacttatcttggttttgattttaatatttttccctaataagtt----gttataccagcag---------------------------------
||| || ||||| |||||||||||||| |||||||| |||||||| ||||| |||  ||| || || |||||| | ||||| || ||||||      |||||||| || |  | |      |     || |||||  |  || |      || |||| |||    ||||| |    |                                  
CATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTACTGGTGATCGAGGTGGTCGAGTGGTTCTCTTTGAGAGAACAGATACAAAAGATgtaag-actattttttgcttatgcaagtgtttttgtgtaaaaaaaaaaaaccaaataggttccttgttatgcacttaatattgtaacatgtatgttttctgaaacatgcag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 2
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagc------accacatgtatgaacttatcttggttttgattttaatatttttccctaataagttgttataccagcag------------------------------------------------------
|||||| ||||| ||||| ||||||||| |||| ||||||||||| ||||| |||   || ||||| |||||||||||||||||||||||     |||||||| |       | ||||||  ||  | | | ||  ||    || |  ||||||     | |   ||  |   |  |                                                         
CATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAGGGATgtatgttgttttatcacatgc-tgtgccttttttttttcattttctcttattttgtttcattttatttctggccttgatttacttctatatcacttcttgttgcaccattttaatgtaattgcataatgtatag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 2
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgtatgaacttatcttggttttgattttaatatttttccctaataagttgttataccagcag---------------------------------------------
 || || ||||||||||| ||||| |||||||||||||| ||||| ||||| |||   || || || |||||| ||||||| ||||| |||     ||||||  |  |    | | | |||    || |  |||  |||   |||     | | ||| ||||   |||                                                   
TATTATTTCTGCAATTGAGTTTGATAAATCTGGTGACCACCTTGCTACTGGTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGATgtgcgttc----ttttttaacactactggtctttagtttctgtatccaaacttgataggttgccttactgttcttgtttctttcaatattatgatatctttatacactgtaatgtgtag

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|19057502|gb|BM736169.1|BM736169
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211386652|gb|FL015625.1|FL015625
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|31352864|gb|CD437221.1|CD437221
EST:     ATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACCTTATGTTCCAGTTACTAGACAC
genomic: ATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|149084056|gb|EE173454.2|EE173454
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|19822590|gb|BQ048614.1|BQ048614
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|4753303|gb|AI657208.1|AI657208
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|148932282|gb|EC875841.2|EC875841
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCCAGCCAG
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCC-AGCCAG
EST: gi|71419454|gb|DR804774.1|DR804774
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|149051574|gb|EE155673.2|EE155673
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211384020|gb|FL015615.1|FL015615
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211386656|gb|FL015629.1|FL015629
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|78112474|gb|DV530868.1|DV530868
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|19057676|gb|BM736343.1|BM736343
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|19436843|gb|BM953253.1|BM953253
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211384023|gb|FL015618.1|FL015618
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|148945029|gb|EC890213.2|EC890213
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211386650|gb|FL015623.1|FL015623
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211384019|gb|FL015614.1|FL015614
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|9732635|gb|BE511387.1|BE511387
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATATTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|50332602|gb|CO527728.1|CO527728
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211386648|gb|FL015621.1|FL015621
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|149076328|gb|EE164942.2|EE164942
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211386655|gb|FL015628.1|FL015628
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         AATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACAC
EST: gi|211384022|gb|FL015617.1|FL015617
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         C
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcag-
EST: gi|211384022|gb|FL015617.1|FL015617
EST:     GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGAT                         C
genomic: GGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcag-

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: 44 (upstream exon), 46 (downstream exon)
Score: 170

CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcacca ... ataccagcagAATGCCAGCCAGAGAGAACTGGAGAGACAAGATGTTCCAGTTACTAGACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgtatgaacttatcttggttttgattttaatatttttccctaataagttgttataccagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG