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

GTGCTAATGCCGATATACATGTCATTCCAAAAATTGAAAGTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccattgatgctggccatgcaatactttgataccaaaagacgtaaattcatagaaagggaaagtacttttaatggtaaaatgagcgtatactttt...

Basic information

species Zea mays
transcript GRMZM2G033526_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 6
GTGCTAATGCCGATATACATGTCATTCCAAAAATTGAAAGTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaag----accattgatgctggccatg-caatactttgataccaaaagacgtaaattcatagaaagggaaagtacttttaatggta-aaatgagcgtatactttt
|||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||    ||||| ||   |||   |  |||    ||  ||  ||||      |  || | | ||| |  |   ||||| |   || |  ||    || |   ||
GTGCTAATGCAGATATACATGTCATTCCAAAGATTGAAAGTGCAGATTCAATACCAAACCTCCAGTCCATTATTGCTGCTTCAGATGGGgtaagtaagaccatggacattggttgtttcaaccagtttgtattaaaa------acatcttggcaagtggcatctcttttcagcatatatttgcctttagatagtt

upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA01G40860.1 (Glycine max), 5'ss of exon 5
GTGCTAATGCCGATATACATGTCATTCCAAAAATTGAAAGTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccattgatgct--ggccatgcaatactttgataccaaaagacgtaaattcatagaaagggaaagtacttttaatggtaaaatg-agcgtatactttt
||  ||||||||||||||| || |||  ||||||||||||||||||||| |||||||| || || || ||  || |||||||||||||||| ||     |  || |  |   ||| | |   | ||||        | | ||| | |   |    |||| | | | |||  ||   || | | | ||  |  
GTCATAATGCCGATATACACGTGATTGTAAAAATTGAAAGTGCAGATTCCATACCAAATCTCCATTCGATACTTTCTGCTTCAGATGGGgttagtttcatactgttcagattatgtattg--tggatatttcgtatcttcaatgccttccagttaaaaggattgtaaatc-tactttgcatcttttaactaa

upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 6
GTGCTAATGCCGATATACATGTCATTCCAAAAATTGAAAGTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagac--cattgatgctggccatgcaatactttgataccaaaagacgtaaattcatagaaagggaaagtacttttaatggtaaaatgagcgtatactttt-
|   |  ||| ||||| ||||| |||   |||||||||||||||||||| |||||||| || || ||||||||| ||||||| |||||||| ||    || |  |  |    |  ||   | | |||     | |    |  |   ||      || || ||    ||| | |||       | |  ||   
GCTGTGGTGCAGATATTCATGTGATTGTGAAAATTGAAAGTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGGgttagttttcagtattcataaagagtcacctcatggatcttttatgcttcacgtatttattgttagacaggaca---aataggaaatgttatatttctttccc

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|22133857|gb|BQ833942.1|BQ833942
EST:     GTGCAGATTCAATACCACACCTGCAGTCCATTATTGCTGCTTCAGATGGG                         GCAATGGTGGCGCGTGGAGACCTTGNG-GCTGAACTTCCGATTGAGGATGT
genomic: GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccat ... atcttttcagGCAATGGTGGCGCGTGGAGACCTTG-GTGCTGAACTTCCGATTGAGGATGT
EST: gi|13177889|gb|BG349072.1|BG349072
EST:     GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGG                         GCAATGGTGGCGCGTGGAGACCTTG
genomic: GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccat ... atcttttcagGCAATGGTGGCGCGTGGAGACCTTG
EST: gi|87155458|gb|DY400247.1|DY400247
EST:     GTGCAGATTC-ATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGG                         GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTT
genomic: GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccat ... atcttttcagGCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTT
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGG                         GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTT
genomic: GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccat ... atcttttcagGCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTT
EST: gi|67016939|gb|CO445688.1|CO445688
EST:     GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGG                         GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTT
genomic: GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccat ... atcttttcagGCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTT
EST: gi|67022089|gb|CO450838.1|CO450838
EST:     GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGG                         GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTT
genomic: GTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccat ... atcttttcagGCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTAATGCCGATATACATGTCATTCCAAAAATTGAAAGTGCAGATTCAATACCAAACCTGCAGTCCATTATTGCTGCTTCAGATGGGgtaagaccattgatgctggccatgcaatactttgataccaaaagacgtaaattcatagaaagggaaagtacttttaatggtaaaatgagcgtatactttt

- - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG