Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaacaccacatatttcgcataggcgtggggtcacagataaacttatgaaaatggcacttcgtatgttgcactatgccagttagggttagggcatg...

Basic information

species Zea mays
transcript GRMZM2G160569_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160569_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g44070.2 (Oryza sativa), 5'ss of exon 2
TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaacaccacatatttcgcataggcgtggggtcacagataaacttatgaaaatggcacttcgta-tgttgcactatgccagttagggttagggcatg--------------------------------
| ||||||||||| ||||||||||| || ||||| ||| |||||||||||||||| |||||||||||||| |||||| | |||||||| || ||  |  | ||| ||||   |||     | ||||||  ||  | ||||||||||| ||     |  |   ||     ||  |||  ||| |                                 
TATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGATCAGGGGCAAACAGTTGGCTTGTCAATTTGGAGgtgagaaatacaccccaattcccatatatgtgaaccgagagataagtttgagcaaatggcactttgtggcactagagattgttgtatatcgttcaggctttagtagctgatggtgattcgtttggaattccag

upper sequence: GRMZM2G160569_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv05s0020g01110.t01 (Vitis vinifera), 5'ss of exon 2
TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgt--gaggaacaccacatatttcgcataggcgtggggtca-cagataaacttatgaaa--atggcacttcgtatgttgcactatgccagttagggttagggcatg
| ||| |||||||||  ||||| ||||||||||||||| | || | ||| ||||| ||||| ||||||||| |  || | |||||  | | | ||   || | ||   ||  | |||   ||| || ||     ||||  |  |||||||||| | | |||   |      |||    ||        
TATGCCTGGATGGAACATTACCTGGTTACCACCTCCACCGGGGATATGGGTCAGGGGCAAATAGTTGGCTCATTCATTTGGAGgtttgtgaagcaaaccaaagttt-tatctgtgtgcactcaacatatgtcactatggcactatggcacttcctttattgttat-catttgttcattttttttt---
















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|211148214|gb|FL118142.1|FL118142
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCYGGTGCAATGATCGCAGSAGCTGTGTGTTTCCGCAAGGGCAG
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTT-CCGCAAGGGCAG
EST: gi|78085961|gb|DV514354.1|DV514354
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGAGGAGGCTGGTGCAATGATCGCACCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|76020752|gb|DT947922.1|DT947922
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|211148217|gb|FL118145.1|FL118145
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAG
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAG
EST: gi|31358086|gb|CD442443.1|CD442443
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGCGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|91051275|gb|EB161693.1|EB161693
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|29167875|gb|CB411135.1|CB411135
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|67013089|gb|CO441838.1|CO441838
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGT-TTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|149110301|gb|EE190341.2|EE190341
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|31910847|gb|CD651628.1|CD651628
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|76932741|gb|DV173142.1|DV173142
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|149014463|gb|EE044079.2|EE044079
EST:     TCCACAGAGGGTTTGGATCAGGAACAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCCATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|148980469|gb|EE027156.2|EE027156
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|31356050|gb|CD440407.1|CD440407
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGCGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|93016717|gb|EB642237.1|EB642237
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|50332178|gb|CO527304.1|CO527304
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|149066716|gb|EE286857.2|EE286857
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|32837292|gb|CD976970.1|CD976970
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGACAATCTCGAG                         GGCGGAGGCTGGTGCATTGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|149085225|gb|EE174733.2|EE174733
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|211148219|gb|FL118147.1|FL118147
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|148953388|gb|EE152882.2|EE152882
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|149028342|gb|EE286117.2|EE286117
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|149101142|gb|EE187250.2|EE187250
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|78075695|gb|DV504129.1|DV504129
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|211149659|gb|FL118150.1|FL118150
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
EST: gi|149009227|gb|EE041332.2|EE041332
EST:     TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG                         GGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT
genomic: TCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGT

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: 51

TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGTCGTCGTGGATCATCAAATCACATGGAGAGGCAACTCCAGTTTACAGGGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 61

TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGTCGTCGTGGATCATCAAATCACATGGAGAGGCAACTCCAGTTTACAGGGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 53

TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGTCGTCGTGGATCATCAAATCACATGGAGAGGCAACTCCAGTTTACAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaaca ... ttgtattcagGGTGGAGGCTGGTGCAATGATCGCAGCAGCTGTGTGTTCCGCAAGGGCAGTCGTCGTGGATCATCAAATCACATGGAGAGGCAACTCCAGTTTACAGGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAGgtgaggaacaccacatatttcgcataggcgtggggtcacagataaacttatgaaaatggcacttcgtatgttgcactatgccagttagggttagggcatg

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagataaa