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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattgaaaagaaaaactaccttgatgtatactgtaagtaaagatgtctgtttaacgtatatgttctcttgcaaaaag

Basic information

species Zea mays
transcript GRMZM2G017386_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017386_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g44110.1 (Oryza sativa), 5'ss of exon 8
TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattgaaaagaaaaactaccttgatgtatactgtaagtaa--agatgtctgtttaacgtatatgttctcttgcaaaaag
|||||| ||  |  ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||| |||||||||||||||| |||||||||   |||||    || ||||||||||||||||  | ||   || |||||  |||| |||   |||||||  
TTTGGTTGCGTTACGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAAGTTGTTAGGATGCTTGAGTCTGAAGAAGTTCCATACCGGGAGgtaatgattgaaaaaccaaact----tgttgtatactgtaagtaataaaattcttgcttaac--atatcttcatgtgcaaaag-

upper sequence: GRMZM2G017386_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G45540.1 (Glycine max), 5'ss of exon 8
TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattgaaaagaaaaactaccttgatgtatactgtaa-gtaaagatgtctgtttaacgtatatgttctcttgcaaaaag------------------
|||||| ||||| |||||| ||||||||||| |||| ||||| ||||| ||| | || ||||| |||||||||||  | || |||   ||||  || |||||     || || |       | |    || ||   | ||  ||  || |      || ||   |  ||  | |  ||||                     
TTTGGTTGCACTCAGGTGTATTGATCCTGACGCTGACAAGAGGCCTAAAATGAGTCAAGTTGTGAGGATGCTTGAAGCTGACGAATATCCATTTCGAGAGgttccc-ttcaatatcttgttttctcacatttaagttctagtgtttagttaatgagttgactcttgagtcttttatcaaatttttgcaactttttgacctt

upper sequence: GRMZM2G017386_T03 (Zea mays), 5'ss of exon 7
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 5'ss of exon 8
TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaagga------------ttgaaaag--aaaaactaccttgatgtatactgtaagtaaagatgtctgtttaacgtatatgttctcttgcaaaaag----
| | || || || ||||||||||| |||||||| ||||||||||| || ||| | ||||||||| | ||||| ||    || |||   ||||  || |||||    |            || ||| |  || || ||  |   ||| || |     ||    |   |  |  |  |  ||  | | ||  ||||      
TCTTGTCGCCCTTAGGTGTGTTGACCCTGACTCAGAAAAGAGACCCAAAATGAGTCAGGTTGTTCGAATGCTCGAACAGGATGAATACCCATTTCGTGAGgtgcttaccaattttctccttcaaatgttaacaattaattacttgtttatttatcttatttctccttactatattttaataattttttataaaattgata

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|60398631|gb|DN231447.1|DN231447
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|148996026|gb|EE035279.2|EE035279
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|5919441|gb|AW054538.1|AW054538
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|211334248|gb|FL383115.1|FL383115
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|5932735|gb|AW057096.1|AW057096
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|32935226|gb|CF040038.1|CF040038
EST:     GGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: GGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|32935252|gb|CF040064.1|CF040064
EST:     GGATGCTTGAGTCAGAAGAA-NACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: GGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|149005056|gb|EE039581.2|EE039581
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|86467803|gb|DY234173.1|DY234173
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|5901151|gb|AW042251.1|AW042251
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGC
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGC
EST: gi|83279062|gb|DV943070.1|DV943070
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|5650293|gb|AI920653.1|AI920653
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAANAAGTNCCATNCCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCNCTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|4646617|gb|AI491437.2|AI491437
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|211277723|gb|FL440066.1|FL440066
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAARAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|93011783|gb|EB637303.1|EB637303
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT

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: 47 (upstream exon), 46 (downstream exon)
Score: 152

TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATTGCAGAGGGTTCCAACTCTGCGGAGTTTGGAAAGAAGGTAGAAAGGACTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 150

TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATTGCAGAGGGTTCCAACTCTGCGGAGTTTGGAAAGAAGGTAGAAAGGACTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATTGCAGAGGGTTCCAACTCTGCGGAGTTTGGAAAGAAGGTAGAAAGGACTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 89

TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATTGCAGAGGGTTCCAACTCTGCGGAGTTTGGAAAGAAGGTAGAAAGGACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGTGGCACTGAGGTGTGTTGATCCTGACTCTGAAAAGAGACCTAAGATGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattgaaaagaaaaactaccttgatgtatactgtaagtaaagatgtctgtttaacgtatatgttctcttgcaaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT